ALTERNATE ENDING IDEA
Hammer group getting overrun. Anderson, realizing that this is the last best chance for victory, decides to retreat for the moment and call in all the stops. Reaper forces rally around Harbinger to prevent the allied forces from boarding the Citadel. Whatever allied forces remain close enough to report to fallback position to prepare for final assault - and will depend on choices one made in prior games as well as EMS.
As Shepard is the crux of the attack, Anderson allows him to make the call on the final assault, Speech ensues. Shep orders final attack.
Cut scenes show Elcor/Assari units attacking Reaper heavies (brutes/banshees), krogan/salarians engaging Reaper squishies (cannibals/husks), with human forces scattered withing both groups. Turians/Merc groups take flanking positions alongside Shep and his teams pushing down the middle. Rachni forces can come into play if available, and cut down on the resistence Shep faces on run to beam. Shep plays final assault in a similar manner as in ME3, but with notable assistants from his/her war assets. Final push takes longer, more enemies, things get desperate on both sides. Harby joined by other Reapers (1-3 perhaps, depending on EMS), forcing the allied forces to bunker down.
Cut scenes show heavy losses sustained in attack. Harby + Reaper buddies keeping things at bay. Shep calls in massive air support from Hackett. Turian/Quarian fleets begin bombardment of Reapers from orbit. Volus bombers join in, taking out the Reapers that joined Harby. If EMS not high enough because the fleets were not aquired, Shep can die at this
point and game ends with cutscene of harvesting throughout the galaxy. If high enough, play resumes as forces are now able to move forward. As player gets close to the transit beam, "final boss fight" ensues.
Player fights waves of Reaper forces, getting help from war assets. If EMS not high enough, Sheps team could take casualties (all squadies part of push, similar to SM, as those not in the current Shep party help lead other allied units into battle), blah, blah, blah) or the assault can fail going to cut of Reapers harvesting and game over. After waves defeated, Shep and whatever is left of his team push toward transit beam, avoiding attacks from Harby on the way. As team approaches beam, orbital fleets - at great cost to themselves - make final assault on Harby, blowing him away while Shep angrily shouts "this hurts you!!!" (OK, added drama not necessary). Before Harby goes the way of the destroyer, he gets off one last burst that either takes out mass of allied troops or most of Sheps team (depending on EMS). Just before Shep steps into beam, he pauses and looks around at all the death and destruction whilst impressive melodramatic music plays in background. You have choice to either step right into beam and move on, or have brief convo with squaddie/LI about the sacrifices the galaxy has made, perhaps even brief flashbacks of good times with squaddies that fell in final assault if EMS not high enough, then step into beam.
Shep has final conflict with TIM, but it can be Anderson or squadmate depending on EMS/choices similar to SM in ME2 helping deal with TIM. Shep defeats TIM (though could be done as actual battle instead of cutscene convo), has chat with Anderson/Squaddie (full one, not the cut one) as Crucible docks and then decides what to do: Finish what TIM started by attempting to control the Reapers or use Catalyst to destroy Reapers (I don't see a problem with the Crucible, I can see and get behind the idea of every cycle before adding something to the HOPE of the future). As the Catalyst finishes docking, Citadel come under fire from the Reapers in orbit. Allied fleets turn on them, attempting save the Crucible project.
TIM choice ends with Shep fully indoctrinated and Reapers win. Cut scenes show harvesting, death, etc, etc.
If Shep chooses to use Catalyst, several branch points can follow due to EMS, including a few where Crucible is destroyed by the Reapers because EMS not high enough. This leads to an extended cutscene showing the Harvesting, the Citadel repaired and back in the orginal position, and after a fade to black we see a strange alien activating Liara's time machine and a few images of Shep in action before final fade-to-black. High enough EMS score allows Crucible to fire, destroying the Reapers.
Anything but EMS maxed out results in Shep sacrificing himself, staying stubbornly behind while the squad evacs, manning the Citadel defenses himself to buy enough time for the Crucible to work. Citadel ends up destroyed, but not before Crucible fires. This ends in cutscenes of Reapers being destroyed,Citadel blowing up, and galaxy mourning their dead. Final scene begins showing species working together to rebuild on various worlds (i.e. Krogans on Palaven, Salarians on new Krogan world, Geth on Rannoch, and all on Earth), and ends with Shep's surviving friends, squad, and Council attending Sheps memorial service.
Maxed out EMS has Hackett telling Shep to evac, as he and his allied fleets can (and do) keep the Reapers at bay. Shep and squad evac to Normandy, and watch as Crucible fires. Cutscenes show Reapers being destroyed before brief fade-to-black (though music continues to play, changing from victorious to melodramatic). Cuts to scene in Sheps cabin. Shep is lying in bed, hands behind head, staring blankly at the ceiling. Flashbacks with poignant music follow, showing (if they occured) Wrex's death, Virmire casualty, Saren's suicide, Hostages dying from BDtS, times with ME2 squaddies that died in SM, Mordin, Thane, Legion.... LI comes in and lays down next to Shep and asks what is wrong. Shep finally comes clean to LI about the nightmares, about seeing the faces of all he wasn't able to save. Shep goes off on the billions of lives that he said he would save but couldn't, about the worlds that are burning because he couldn't make the Council listen. Shep finally cracks from the strain of the trilogy, asking as he walks to the window with the clearly viable Earth still burning below, how he can live with him/herself for being responsible for so much death and destruction, the friends and loved ones lost in the battle. Perhaps Shep can even crack enough to collapse in the arms of his LI in tears as the pain washes over. LI says some comforting words about how many trillions survived and will continue to live thanks to Sheps efforts. Shep responds with a hollow sounding thanks and maybe another hug and kiss, depending on a player choice. Scenes then show rebuilding efforts, Citadel still in Earth orbit (Council would decide to leave it there as a monument to galactic unity), and Shep receiving honors from the Council. If Shep has no LI, Anderson can be replaced, and the dialog would change to reflect that.
Why would an ending like this be a "magical happy ending" or "rainbows and unicorns"? Just because there is an ending where Shep lives with squad and LI all alive doesn't mean that ending has to be all wrapped up in a pretty package.