I am not as upset by it as I could be. It was never going to be straightforward, there always had to be some sort of twist, so the fact that the ending wasn't "and then we slugged the reapers to death with very large bullets" doesn't trouble me. The fact that the crucible was something really weird doesn't trouble me.
The reveal about the reapers themselves bothers me. I was really hoping they weren't going in the direction of "reapers are archived sentient minds" because that is pretty silly and takes a lot of the eldritch horror out of them, taking them from unfathomable to nonsensical. Why would a few million human minds suddenly sign on to the galactic murder train just because you put them in a cuttlefish?
The purpose of the reapers troubled me more. Both because there was a purpose (I liked them better when they were ineffable) and also because of the choices given to me to react to that purpose. Like, okay, the citadel AI believes that synthetics will always wipe out organics, so it gives me these three choices. I can get behind that. That makes sense. However, what the hell was the point of the Geth and EDI storylines if I can't turn to the AI and say "Uhh, actually, I totally got the synthetics to play nice, and now they're invited to all of our sexy organic parties. The geth send me yearly christmas cards. Can we try rethinking our base assumption here?"
The fact that Shepard just accepts that "okay, yeah, synthetics will always wipe out organics because the shimmery space gradeschooler says so" completely gives the lie to what she was saying through the entire rest of the game. If I had to pick one thing that bothered me, it's that.
That said, I feel like we're being set up for some serious End-of-Eva nonsense. And frankly, I'm totally on board if that's the way they want to go with it. In that light, the entire scene on the citadel takes on the character of a...statement of intention. You aren't actually changing anything, but within the dream/vision sequence you're choosing what you want from a conclusion. Proving yourself to something that's judging you based on what you choose. Interesting to see if they'll build on that.
Suddenly, I find myself wondering if the inclusion of a character named "Eva" toward the beginning was meant to be reference.