Not having as many squadmates as in ME2. One of my favorite aspects of ME2 was having this diverse range of interesting characters to choose from.
In 3... you had Garrus, Liara, and a bunch of humans and EDI who was nowhere near as awesome as Legion.
And no I don't care about bullshit DLC characters.
-
Mainly Cerberus. They got turned into generic evil bad guys. I wish there was a way to support them more. I also didn't like how predictable the game was. I replayed the series recently and had a blast playing ME 1 and 2. When I got to 3 I stopped because it got boring and slightly comedic.