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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While I loved the game, I wish the side quests involved more than scanning random planets for some guy's shit. Also, too much auto-dialog, I like being able to micromanage shepherd's dialog.