Trap.
I've read a lot of comments saying things like "95% of ME3 is fantastic, but the other 5%..." or "ME3 was everything we could have hoped for, up until the last ten minutes". I disagree. I'm not saying its bad, by any stretch, but it has other problems as well, even if they're overshadowed by the collosus of the ending. And the Crucible is the worst of them. It alone would make ME3 the worst of the series, even without the horrible, horrible ending. But it can be fixed. Even better, it can be fixed as part of fixing the ending, and the fix for one flows naturally into the fix for the other.
What is wrong with the Crucible? Everything:
Oh look, lost prothean plans for a superweapon that can defeat the Reapers. Unlikely.
Wow, and we found them at exactly the same time that the Reapers attacked. Ridiculously unlikely.
And we don't know what it is, what it does or how it works, but we're pretty sure it'll destroy the Reapers. Why, exactly?
And these plans written in a millenia dead alien language are so easy to read. Uh, sure.
And Vigil never said "Oh, and if you don't get there in time to stop Saren, the only other chance you've got is to complete the crucible". Apparently VI stands for Village Idiot.
And the beacons that were so important back in ME1 neglected to mention this incredibly convenient device. Probably programmed by the same morons as Vigil.
Then it goes beyond the implausible and the silly and gets into true Whiskey Tango Foxtrot territory:
It wasn't designed by the Proteans after all, it was designed by an untold number of species over the course of aeons. Even though none of them knew what it was or how it worked.
And every single cycle, despite the builders and most of their technology and records being wiped out by the reapers, the plans still managed to survive and get passed on.
And somehow, despite having NFI how this thing works or what it does, we are certain that all we need to complete it is the mysterious 'catalyst'. Once again, why are we so sure?
And despite the fact that nobody but the keepers and the reapers really has a clue how the Citadel works, and the fact that nobody knew the Citadel was the catalyst, the Catalyst and the Crucible connect and interface perfectly.
Is there a single 'fact' revealed about the Crucible at any point in the game that isn't, at the very least, unlikely, and at the extreme, bordering impossible? (And I think I'm being charitable including the word 'bordering')
Finding something like this right now is too good to be true. It's too convenient. It's like fleeing a battle station the size of a moon and being pursued by only four unshielded fighters...
Admiral Ackar can draw the obvious conclusion from all this.
IT'S A TRAP!
Here's my alternate theory:
The Crucible is yet another Reaper backup plan.
It is not passed from victim race to victim race, but instead planted by the reapers each cycle.
Eva was not on Mars to recover the plans, she was there to plant them. Acting on the orders of Harbinger, via his little **** TIM. (or if you don't think TIM is sufficiently indoctrinated so early, then Harbinger plants the plans where Cerberus will find them, then manipulates TIM into thinking that it'd be a great idea to plant the plans on the Alliance and let them take care of the hard work of building the damn thing).
Why would the Reapers do this?
Easy. Because it gives all your victims a false hope to cling to and work towards, wasting all their resources on a pointless piece of junk instead of putting their clever little heads together and coming up with something that could really hurt you. Like, I dunno, a way to sneak onto the Citadel and disable it, stranding your entire race in Dark Space. Because if you keep those meddling kids busy chasing red herrings, you might just get away with it.
Occam's Razor is definitely on my side.
The next bit is more tenuous and speculative, but is where everything connects in to fixing the ending.
So far, I've assumed that the crucible is nothing but a red herring. A great big machine that does nothing but waste resources (and go ping). But I think it's more likely that the Reapers would kill two birds with one stone by having their victims build something for them. Plus there's a sort of vicious humour to be had in the idea that the epic project that the victims believe to be their only hope is in fact the very thing that will destroy them.
What do I think it does? I think it makes Reapers.
Not the bodies. We've seen a little of how that's done in ME2. I think the Crucible creates the mind of a Reaper. This doesn't just come from nowhere, of course. It's built and corrupted from the minds of one or more organics. It's like indoctrination to the nth degree. The crucible is both the means of their conversion and the process of their selection. Only the best, brightest and boldest could ever complete and trigger the crucible, and that's exactly who the Reapers want.
I can't imagine what the full process of conversion might involve, but I can imagine how it might start. You offer the victim a choice:
Control the Reapers - And he begins to think of the Reapers as being an ally rather than a threat.
Merge with Synthetics - And he begins to accept the idea of being an organic/synthetic hybrid. Such as a Reaper.
Destroy the Reapers, but also destroy some of your own allies - And he accepts the idea of genocide being acceptable as a means to an end. And you've got him thinking like a Reaper already...
It's an Iocaine Gambit: every choice is toxic. The only winning move is not to play.
So how does this help us fix the game? Well, I'm not going to try and write a new ending in any depth, but here's my brief proposal:
We play out exactly the same as before. But when we're offered the RGB poison, we reject it. We tell the catalyst to shove its 'choices' up its presidium. Cut to groundside. The player is now in control of Anderson (with Coats as squadmate). We play through the conduit rush again from their perspective. We see Shep go down. Before we can get to her, a Brute appears. Grabs Shep surprisingly gently and carries her into the beam, which promptly turns off. Hammer's in rough shape, but a voice comes over the comms: Major Kirrahee. "Hold the line, Hammer. Help is coming." Epic battle ensues, showing some of those hard won war assets: Krogan cavalry, Liara's Commandoes, Elcor Heavy Infantry, Salarian STG, Aria's Blood Pack, Jack's Biotic Artillery, pretty much any ground troops on the war assets list (damnit Bioware, we earned this), maybe even use some of our own multiplayer characters. Hammer is successfully extracted, Anderson gets to kill a Reaper. Using the Ilos Conduit, a daring rescue plucks Shep from the Crucible. Shep reveals what was being done to her and what the crucible really is.
Okay, so we've got Shep back, we've retconned the inane ending into a Reaper mind-game, and we've established that the Crucible is a trap, although not all the details have come out yet. From here, there's a thousand ways the story could go, so if you don't like the rest, I'm not so bothered.
We track down the illusive man, find out what he knows about the origin of the crucible plans and kill him (cutscene or dialogue, not boss battle). With this intel and the plans from Mars, our techs develop a way to frack with the Crucible. With a little modification, it can be turned against the Reapers, attacking them mentally and damaging their indoctrination. The personality that was turned into the dominant mind of the Reaper can regain control. There's only one thing. Shep will have to go back to the Citadel. And this time the Reapers will be on guard. Epic space battle to get onto the Citadel, featuring (once again) those War Assets we wasted so much time collecting. Harbinger will be the boss battle, in his shiny new robot form (similar concept to EDI, but a lot bigger and nastier). After the fight, Shepard uses the repurposed Crucible. Effect depends on War Assets. Specifically on the scientists, engineers, technicians, etc. The stronger your analysis/design team, the more effective their modifications to the Crucible. At worst, the Reapers falter before reasserting control. At best, the Reapers are thoroughly defeated in one fell swoop.Various degrees of middle ground, with the most common one being that some Reapers remain free, most convert back, leading to Reaper civil war, which even if the deconverted reapers lose, will soften them up to the point where the galactic alliance can actually win the war head to head.