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.
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The same thing that has disappointed me throughout the entire series: you amass a sizable amount of followers, only to have them sit around your ship the entire game being utterly worthless. The only time in the series where I didn't feel like I was Papa Shepard bringing home dinner to a bunch of helpless children was during ME2's suicide mission, when your crew finally got off of their lazy asses and finally helped you do something.