YouTube's People Make Games asked several ex-BioWare developers who worked on Mass Effect 3 how they felt about the endings, and in particular about putting together the Extended Cut—an update that expanded on the endings and addressed some of the many complaints players had. It's a great video and worth a watch, especially for the section where it highlights the additional crunch developers had to go through to pull the Extended Cut together, after already crunching to complete Mass Effect 3.
But before that, it also explains that during development much of the team didn't know how Mass Effect 3 would end. "A lot of us didn't have a whole lot of high visibility into what the ending was actually gonna be," says cinematic designer John Ebenger. Gameplay designer Manveer Heir explains the ending "came in really late" and for a long time before that, only an animatic—the video equivalent of a storyboard—existed.
While we've previously heard about a version of Mass Effect 3's ending planned by Drew Karpyshyn before leaving BioWare, this animatic version seems to have been created after that, and remained in place until the actual ending was written. It's got a lot of similarities to the ending we ended up with, but also some significant differences. Like, instead of the Catalyst, aka the Star Child, the annoying AI who shows up with a reductionist take on the inevitability of conflict between synthetic and organic life at the finale, there was a Reaper Queen.
This ending begins with Shepard arriving on the Citadel, which has fused with the mysterious superweapon called the Crucible, and jacking in. As animation director Dave Wilkinson puts it, "At that point Shepard was so augmented with like electronical bits and all the rest of that kind of shit, I actually had him just plug himself into the Citadel." Shepard enters "a virtual world" and meets what was described in the notes by project lead Casey Hudson that Wilkinson was working from as "like the God of the Reapers. I think it was a queen?"
The Queen explains that she's been imprisoned by her servants for arguing that their cyclical destruction of civilizations wasn't sustainable. She'd say, "'We have to evolve, but we're incapable of evolution because of the limitations of our AI,' and stuff like that. She was their queen, but she proposed things the reapers didn't like, so they locked her away inside the Citadel and just never ever listened to her again. And so the conversation was her going, 'This is a chance to evolve everything. Like, we can move everything forward.'"
From there, players would have the traditional three options for their preferred flavor of ending. "The renegade option was, Shepard's just like, 'Go fuck yourself.'" After that, Shepard leaves the simulation, and sets off the Crucible by blowing up the Citadel. This destroys the reapers, though at great cost—not the loss of all synthetic life, as in the final game's Destroy ending, but rather the Earth being wiped out in the explosion.
"And the paragon option," Wilkinson says, "was 'I'm so awesome I can take control of these reapers and I'll use them for the right reasons.' So then you, Shepard, turned into the big King Reaper. You still said 'fuck you' to the Queen." From there, it's pretty similar to the Control ending, with Shepard using the reapers for good.
The final option was the Synthesis ending, but instead of being the most difficult to obtain, and therefore coded as the 'best' option, it would be "the ending everybody could get", with the others presumably relying on how many paragon or renegade points you earned. As Wilkinson says, in this ending "the Queen was like, 'We're gonna use space magic, and we're gonna combine the best parts of you and the best parts of me and we're gonna send that out to the universe and it's gonna change everything." Which sounds just as nonsensical as the version we got.
Wilkinson doesn't mention whether these endings would involve the mass relays seeming to be destroyed, or the Normandy crashing on a random garden world that happens to be nearby, but otherwise these endings broadly map to the ones the finished game had. Still, not having the AI that looks like a ghost kid and makes a weaksauce argument that synthetics and organics are doomed to never get along seems like it would have gone down at least a little better.