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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I was disappointed by the little exploration on offer, and the seriousness of the story took away the from the fun that me2 had. The dialogue was so much more linear than it should have been. I was impressed by the multiplayer, but the matchmaking speeds were poor and i didnt like the random boxes and how long it took to get enough credits for the big ones.