First, let me get this out of my system. That trophy sure sparkles nicely in the Colorado sun.

Back on topic: I keep bringing this up, but the dark energy plot shown through. To this day, it's one of the only times that I was yelling at my screen and telling BioWare to take a flying leap. Next time, why don't they keep a plot that isn't dependant on one writer leaving? That would be nice.
This is more of a problem with BW as a whole, but a non-crazy brainwashed humanoid villain. I've been thinking about it as I've been replaying the ME series, and it's getting ri-donk-ulous. Unless I'm mistaken, pretty much every major villian in the ME series that was humanoid had something wrong with them. Either they were indoctrinated or drugged or just crazy in general. Even the AI in ME1 (the one stealing credits from the casino) acted like they had lost their mind. Er, so to speak. Hell, TIM was also indoctrinated, because Odin forbid that he couldn't have been just power hungry.
Freedom to use all of my squad members. I'm going back to Legion. If you do more than 3 quests with him, regardless of length, you will be forced into the Abduction sequence. I tend to do Tali's mission at that point, because I love the reactions from the Quarians. Sadly, if you do his loyalty mission, you get the "Take the shuttle" message. No choice. Hopefully, no more invisible timers like that.