Damn, I need to rant about this with company, so thanks in advance for reading. Spoilers ahead.
I have a (bad) habit of replaying these games on a yearly basis. There's mutiple reasons, the most prominent perhaps is the fact that up until the end of the third game, they are so engaging and fun, the stakes are always incredibly high and ultimately, your decisions really shape the world around you. Curing the genophage, saving the geth, destroying the collectors, defeating Sovereign - it's slop, but it's fun slop.
Then you get to Earth by the end of the games and everything starts falling apart. The "beam" between Citadel and Earth is suddenly called "the conduit" by everyone and there is no explanation for it, and it's not like there wasn't the conduit in the first game. At the very end, once the crucible is activated, nobody apart from Shepard knows what the thing does. Still, the fleets are all fleeing, including the Normandy, but nobody knows what's going on. That probably includes the players by that point.
There is so much more in between these examples, but I don't have the beans to go over all of it. It's just a fucking mess.
How did they remove indoctrination theory? Last time I played it, they still had hallucination(?)-TIM insisting that Control is the best ending and you should do it because it will totally work this time, which seems like strong evidence that either Shepard has been indoctrinated or the writers think we're dumb. And although there were some other baffling writing decisions in 3, the rest of the game overall didn't give me the impression that the writers think we're dumb, so it must be the indoctrination thing.