Here's my quick and
dirty flawless redraft of the ME2 ending, swapping in the original draft. Ransom, gimme your take on this.
Shepherd and her team reach the core of the Collector base, where they find a Reaper embryo that looks like the thing on the left:

It is floating free instead of being supported by four crappy little red glowing pipes. There are lots of big ol' cables like creepy umbilicals connected to its hull.
EDI explains that it has a fully functioning mass effect core, and that overcharging that core will destroy the entire base. (This removes the need to have a base-destroying reactor in a floor panel on a random hexagonal platform.) However, she will need direct access to the immature Reaper's systems to trigger the overload.
Shepherd is freaked out by this, but ultimately convinced. The final boss battle involves no giant Terminator making Transformer noises and playing peek-a-boo; instead your team jumps onto the Reaper's hull and moves around it, fighting Harbinger and getting EDI a hard link. There is actually a Praetorian to fight.
In a moment of horror, EDI explains that she has found all the missing colonists. They are alive inside the Reaper. Shepherd demands to get them out, but EDI explains it is only their minds, stored inside the Reaper - tens of thousands of colonists, transferred not by some bull**** 'raw genetic material' pipe that gives the Reapers their 'essence', but by the destructive dissection of their minds. But they are, EDI senses, no longer quite human... (Bear in mind this could be what's happening in ME2 already, it just wasn't revealed.)
The Illusive Man makes his call. He wants the Reaper intact. One of your squadmates suggests it'd be a crime to kill all these colonists. Another says they are already dead; whatever the Reapers have done to them, it'd be a mercy to end their suffering.
Shepherd makes her choice: overload the Reaper's mass effect core, destroying it and the base, or set it to emit a radiation pulse, killing all the Collectors but leaving the Reaper and its posthuman cargo intact.
Voila. All the horror of the ME2 ending retained - you can still have people disintegrating juicily in pods, because we could say their brain matter is used for part of the Reaper design, just as human brain matter is used in the Scions or Praetorians. And none of the crap!
nuuu ransom read the thread and LEFT
he HATES it
And Jeff Vader hates double-posting. *****.