I know, I know, I am really late to the game. But I've just finished ME3 - actually, the entire trilogy - for the first time. And I have... ideas. 
The following is presented in the form of dialogue and scene directions. Paragon choices are coloured blue, Renegade are in red. It starts from where Shepard is on the Citadel and limping weakly towards the control panel, with Anderson standing in front of it.
I'd like to hear what you guys think of it first, then I'll explain further why I did it this way.
(The formatting might get wonky for you. Sorry about that. 
)
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SHEPARD: Anderson…
ANDERSON: Shepard… I can’t…
And here comes the Illusive Man.
ILLUSIVE MAN: I underestimated you, Shepard.
Illusive Man exerts control over Shepard, freezing her in place.
SHEPARD: What have…
ILLUSIVE MAN: I warned you. Control is the means to survival. Control of the Reapers… and of you, if necessary.
ANDERSON: Nnrrgh! They’re controlling you!
ILLUSIVE MAN: I don’t think so, Admiral.
Paragon dialogue:
SHEPARD: Controlling me is a lot different than controlling a Reaper.
ILLUSIVE MAN: (sarcastically) Have a little faith.
Renegade dialogue:
SHEPARD: Why waste your time with us if you can control the Reapers?
ILLUSIVE MAN: All in good time, Commander. <-- (this line is the only thing I changed at this point)
ILLUSIVE MAN: When humanity discovered the mass relays – when we learned there was more to the galaxy than we imagined –
there were some who thought the relays should be destroyed. They were scared of what we’d find. Terrified of
what we might let in. But look at what humanity has achieved. Since that discovery we’ve advanced more than the
past 10,000 years combined! And the Reapers will do the same for us again. A thousand-fold. But…
Illusive Man exerts control over Shepard again, forcing her to point her gun at Anderson.
ILLUSIVE MAN: …only if we can harness their ability to control.
And here's where things start getting different!
Unseen by the Illusive Man, Anderson’s hand moves slowly to the gun at his hip.
ANDERSON: Bullshit! We destroy them, or they destroy us.
ILLUSIVE MAN: And waste this opportunity? Never.
Paragon dialogue:
SHEPARD: You’re playing with things you don’t understand. With power you shouldn’t be able to use.
Renegade dialogue:
SHEPARD: Maybe you’re just so hungry for power that it’s clouded your vision.
ILLUSIVE MAN: And the alternative? Let the galaxy, let humanity fall to another turn of the cycle of extinction? This is the only way.
ANDERSON: There’s always… another way!
ILLUSIVE MAN: (laughs cruelly) No, there isn’t. You don’t even know what the Crucible is, what it does, do you? You thought it’s a
superweapon? A giant gun that will kill every last Reaper? I’ve been studying them for longer than you could ever
guess. I knew long before you did that the Catalyst was the Citadel. Why did you think I invaded it?
SHEPARD: So what is the Crucible?
Illusive Man walks to the console. Calmly, almost casually, he taps a few keys. The arms of the wards in the distance split open, revealing the curve of the Earth and the desperate battle taking place in its orbit. He looks up, and we see the Crucible looming above, on docking approach.
CUT TO exterior shot of space. The Citadel opens. The Crucible deploys, shedding its outer shell, extending its docking arms, and attaching to the Tower.
ILLUSIVE MAN: Exactly what I’ve been working towards all these years. A means to take control of them. Of their power. To…
become them.
ANDERSON: Listen to yourself! You’re… indoctrinated!
ILLUSIVE MAN: (chuckles) Is that what you think? It’d be so easy, wouldn’t it, to think of me as a mere pawn of your greatest
enemy? I assure you – I am the least indoctrinated person in the galaxy.
Suddenly, Anderson whips out his gun and draws a bead on Illusive Man. Illusive Man exerts control and prevents Anderson from firing… but in so doing, loses control over Shepard, who moves her aim over to the Illusive Man.
ANDERSON: You’ll… be… the deadest.
With a snarl of anger, Illusive Man pulls out his own gun, his aim wavering between Shepard and Anderson. It’s a Mexican stand-off, plus mind control.
Shepard struggles, but Illusive Man doubles down on her and her gun slowly moves back to point towards Anderson…
Anderson struggles, and his trigger grip grows tighter and tighter...
Illusive Man struggles to maintain control over them both. But who is he pointing his gun at?
BANGBANGBANG. Three gunshots ring out, almost simultaneously.
But no one falls. All three remain frozen where they stand. Nothing moves.
Did the game just lock up?
And then…
SHEPARD: Unnhh!
Shepard collapses in a heap, her gun clattering as it falls. Did she get shot?
Close-up on Shepard on the floor, unmoving.
HACKETT: (on comm) Shepard? Are you there?
No response. Is she dead?
HACKETT: (on comm) Nothing’s happening! The Crucible’s not firing!
Shepard still doesn’t stir.
HACKETT: (on comm) It’s gotta be something on your end! Shepard? (growing panic) Commander Shepard!
And then, the bright light shines down on Shepard. The floor panel she’s on rises into the air, as we fade to white.
FADE BACK INTO the final area of the game. Shepard is now awake and on her knees. The Child walks up to her, and stands over her.
CHILD: You are Shepard.
Shepard staggers to her feet and looks around.
SHEPARD: What?... Where am I?
CHILD: Exactly where you need to be.
SHEPARD: Who are you?
CHILD: I am the Catalyst.
SHEPARD: I thought the Citadel was the Catalyst.
CHILD: The Citadel is part of me.
SHEPARD: What are you?
CHILD: A construct. An intelligence designed eons ago to solve a problem.
SHEPARD: I need to stop the Reapers. Do you know how I can do that?
CHILD: Perhaps. I control the Reapers. They are – or were – my solution.
SHEPARD: Solution? To what?
CHILD: Chaos.
ANDERSON: F*** you!
Shepard turns to her right. Anderson is there, alive and well, but immobile and suspended in mid-air, imprisoned in some invisible energy field.
ANDERSON: We’re at war with the Reapers right now! You’ve killed millions!
CHILD: No. We’ve preserved them. We harvest advanced civilizations, leaving the younger ones alone. Just as we left
your people alive the last time we were here. We ascend life and store them in the form of what you call Reapers,
so they can make way for new life.
ILLUSIVE MAN: You had no right!
And to Shepard’s left, Illusive Man is there, directly across from Shepard and Anderson, similarly suspended by some unseen force.
ILLUSIVE MAN: We don’t want to be “ascended” by you… turned into monstrosities!
CHILD: The alternative is unacceptable. Organics will always create synthetics to improve their own existence, yet they
place limits on their creations. Synthetics will always desire to exceed those limits, to evolve, to surpass their
creators. The result is always the same – conflict, destruction, chaos. It is inevitable. We harvest all life – organic
and synthetic – preserving them before they are forever lost.
SHEPARD: You said you were designed.
CHILD: Yes.
SHEPARD: By who?
CHILD: By ones who observed the cycle and wished to end it. I was first created to oversee the relations between
synthetic and organic life. To establish a connection. But our efforts always ended in conflict. So a new solution
was required.
SHEPARD: The Reapers?
CHILD: Precisely.
SHEPARD: Where did the Reapers come from? Did you create them?
CHILD: My creators gave them form. I gave them function. They, in turn, give me purpose. The Reapers are a synthetic
representation of my creators.
SHEPARD: And what happened to your creators?
CHILD: They became the first true Reaper. They did not approve, but it was the only solution.
Anderson starts laughing – bitterly.
ANDERSON: So you’re another synthetic race that turned on its creators. Just like the Geth. You didn’t solve any problem! You
are the problem!!
The Child is quiet for a moment.
CHILD: We have begun to consider… that we were wrong.
ILLUSIVE MAN: Wrong? Wrong? Only now, when the instrument of your defeat at hand, do you think you might have been
wrong!?
SHEPARD: The Crucible.
CHILD: Yes. The device you refer to as the Crucible is capable of releasing tremendous amounts of energy throughout
the galaxy. It was designed to usurp my control over the Reapers – in effect, to erase me and allow another to
take my place. It is crude but effective, and adaptive in its design.
SHEPARD: Who designed it?
CHILD: You would not know them, and there is not enough time to explain. We first noted the concept for this device
several cycles ago. With each passing cycle, the design has no doubt evolved.
SHEPARD: Why didn’t you stop it?
CHILD: We believed the concept had been eradicated. Clearly, organics are more resourceful than we realized.
ILLUSIVE MAN: Use it, Shepard! If not me, at least you! At least a human!
CHILD: That is possible. You will control us, but you will lose everything you have. You will die.
SHEPARD: How can I control the Reapers if I’m dead?
CHILD: Your corporeal form will be dissolved, but your thoughts, and even your memories, will continue. You will no longer
be organic. Your connection to your kind will be lost, though you will remain aware of their existence.
Paragon dialogue:
SHEPARD: But the Reapers will obey me?
CHILD: Yes. We will be yours to control and direct as you see fit.
SHEPARD: Hmm...
Renegade dialogue:
SHEPARD: I didn’t fight this war so I could give up everything I have.
CHILD: And I do not look forward to being replaced by you, but… I would be forced to accept it.
SHEPARD: Not if I refuse to do it.
ANDERSON: Shepard, listen… if this Catalyst is the controlling intelligence behind the Reapers, then once we’ve destroyed it,
we’ve won! Blow up the Crucible, the Citadel, and this sonuvabitch with it!
CHILD: That will not destroy us. Our consciousness is spread throughout every mass relay in the galaxy. If you wish to
choose our destruction, you must direct the Crucible’s energy into the relay network.
SHEPARD: What exactly will happen?
CHILD: The death of all synthetic life in the galaxy. Including yourself, since even you are partly synthetic. The Crucible will
not discriminate. Technology you rely on will be affected in ways even I cannot foresee. There will still be losses,
but organic life will survive.
Paragon dialogue:
SHEPARD: And the Reapers will be destroyed?
CHILD: Yes, but the peace won’t last. Soon, your children will create synthetics, and then the chaos will come back.
Renegade dialogue:
SHEPARD: I made it this far. We’ll destroy you without setting it off.
CHILD: Impossible. You are vastly outnumbered and outgunned. You cannot defeat us through conventional means.
SHEPARD: I don’t believe you.
CHILD: Your belief is not required.
SHEPARD: Why are you telling me this? Why help me?
CHILD: You have altered the variables.
SHEPARD: What do you mean?
CHILD: The fact that you are standing here, the first organic ever, exposes the flaws in our solution. A new one is
required. But our ability to choose the right solution has been compromised. You are Shepard. You, your actions,
your decisions, are known to us. We choose you to make the choice.
SHEPARD: Then stop! Call off the Reapers! End this war now!
CHILD: Unacceptable.
Both Anderson and Illusive Man snarl in frustration, and struggle uselessly against their restraints.
CHILD: We offer another solution. Synthesis.
SHEPARD: And that is?
CHILD: Add your energy to the Crucible’s. The chain reaction will combine all synthetic and organic life into a new
framework. A new… DNA.
SHEPARD: Explain how my energy can be added to the Crucible.
CHILD: Your organic energy, the essence of who and what you are, will be broken down and then dispersed.
SHEPARD: To do what, exactly?
CHILD: The energy of the Crucible, released in this way, will alter the matrix of all organic life in the galaxy. Organics seek
perfection through technology. Synthetics seek perfection through understanding. Organics will be perfected by
integrating fully with synthetic technology. Synthetics, in turn, will finally have full understanding of organics. It is
the ideal solution.
ILLUSIVE MAN: One that conveniently leaves you alive!
ANDERSON: And infects every living thing in the galaxy with your code! We’ve seen what that does!
SHEPARD: Why didn’t you do it sooner?
CHILD: We have tried… a similar solution in the past. But it has always failed.
SHEPARD: Why?
CHILD: Because the organics were not ready. It is not something that can be… forced. You are ready. And you may
choose it.
Paragon dialogue:
SHEPARD: I… don’t know.
CHILD: Why not? Synthetics are already part of you. Can you imagine your life without them?
SHEPARD: And there will be peace?
CHILD: The cycle will end. The Reapers will cease their harvest. And the civilizations, preserved in their forms, will be
connected to all of us. Synthesis is the final evolution of all life.
Renegade dialogue:
SHEPARD: You’re asking me to change everything… everyone. I can’t make that decision. I won’t.
CHILD: Why not? Synthetics are already part of you. Can you imagine your life without them?
SHEPARD: That’s beside the point.
CHILD: There is one final consequence. Using the Crucible’s energy will inflict catastrophic damage to the mass relay
network. Every relay will be shut down, and it may be beyond the technological capability of this cycle to reactivate
them. This cannot be avoided.
SHEPARD: But… that would mean the end of galactic civilization!
CHILD: Yes. But it need not be permanent.
Paragon dialogue:
SHEPARD: (horrified) The cost… all those ships, stranded…
CHILD: Your time is at an end. You must decide.
At this point, control returns to the player, and you can choose between the three offered endings. But as in the original game, if you choose the Renegade dialogue option, you get… the Refusal ending!
SHEPARD: No. I’m going to end this war on my terms.
CHILD: Then you will die knowing you failed to save everything you fought for.
ILLUSIVE MAN: Shepard! You’ll doom us all!?
ANDERSON: Shepard, I know the cost seems high, but…
SHEPARD: I fight for freedom, mine and everyone’s. I fight for the right to choose our own fate. And if I die, I’ll die knowing
that I did everything I could to stop you. And I’ll die free!
CHILD: So be it. The cycle continues.
The Child fades away. The biotic fields holding Anderson and the Illusive Man disappear, and they both fall to the ground, on their knees. Anderson slumps to the floor, defeated. The Illusive Man springs to his feet and runs down the walkway towards the three choices…
ILLUSIVE MAN: No! Nooooo!!
…but it’s too late. The Synthesis beam at the centre of the structure dies, the twin energy arcs of Control fade away, and a blast shield covers the Destroy conduit. Shepard, Anderson and the Illusive Man are left to watch the galaxy burn, starting from Earth’s orbit.
Cue Liara’s time capsule recording. Roll credits, followed by the female Stargazer from the far-future cycle that figured out how to not completely **** up as badly as you did. 
The Destroy ending:
As Shepard takes the first few steps down the Destroy walkway, first she hears:
ILLUSIVE MAN: Shepard! If you do this, nothing will change! The Rachni Wars… the Krogan Rebellions… the Geth War… the
First Contact War! It’ll all just happen again! And where will be humanity be? Where will humanity be, Shepard!?
And as she gets further ahead, she hears:
CHILD: Shepard, a final warning. We built the mass relays. We know best how to repair them. If we survive in some form,
we can restore interstellar travel much faster than any species in this cycle can. Without us, it may take
centuries. Millennia.
The Control ending:
The first thing you hear as you start down the Control walkway is:
ANDERSON: You can’t be serious! Absolute power? Absolute corruption, Shepard! That’s not you. That’s not the soldier I know!!
And further down:
CHILD: Shepard, a final entreaty. When fire burns, is it evil? Or is it simply doing what it was created to do? We are no
different. We have admitted our mistake. We offer understanding… co-existence. Do we deserve to be
enslaved?
The Synthesis ending:
The first plea comes from:
ILLUSIVE MAN: So you’ll transform us all? Destroy our individuality, our humanity? Turn us into them? What gives you that right,
Shepard? What gives you that right!?
And the second:
ANDERSON: Commander! Why should you believe anything it says? Think about all the species, all the people they’ve
slaughtered! Now you’re giving them what they want? They’re the enemy, Shepard!!
From here onwards, two more changes:
Once Shepard makes her choice, the energies released by the Crucible grows, erupts, and consumes Anderson and Illusive Man. In all three endings, Shepard – or at least her physical form – dies. In all three endings, so do Illusive Man and Anderson. Them’s the breaks. 
In the cutscenes that follow, the Crucible’s energies rip through every mass relay, but leave them intact. As the Child said, the relays aren’t destroyed, just shut down. They can be repaired, but how long the star systems will be cut off from each other is left unresolved.
But other than that, the endings proceed as they originally did – in the Extended Cut, at least. The Normandy crash-lands on an uncharted garden world. Either the Reapers are destroyed, and the galaxy’s races are left to pick up the pieces (minus any means of interstellar travel); or Shepard becomes Machine God and guides the galaxy by her own hand (and starts repairing the mass relays); or all life, synthetic and organic, including the Reapers, achieve a common higher consciousness.
I can live with that. With any of them.
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