I still dislike the lack of a journal hotkey, though that's a minor thing.
The whole "reapear alertness" thing is rather silly and unnecessary. Indeed, the fetch quests in general were ridiculous filler.
More squadmates would have been very nice. I can understand that Wrex can't very well pack his bags and join you on the Normandy, but why not Grunt? Samara? Jack? Garrus and Liara are among the two best characters in the series but more characters = more fun.
The ending (less said there the better. Though the theory improves things enormously, it means that the ending is incomplete).
The ending aside, I only have minor complaints about the game. There are some brilliant moments, the story is beautifully told, and the gameplay is as satisfying as ever. I love the new twist brought by the multiplayer.
Having said that, I didn't feel that previous decisions really tied in very much to this game. Killed the rachni queen? Meh, here's a robot rachni queen. Killed the council in ME1? The salarian kind of likes you a little more. Destroyed the collector ship in ME2? Apparently not. They were too scared of making you feel the consequences of your actions.
(Former) Lead Moderator and (Eternal) VGC Detective 
