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 fact that a majority of the side missions were nothing more than going to a star system and spamming the scan button over and over. The first one at least had exploration of uncharted worlds. Yeah, they were just random terrain maps colored blue, but at least it was actual gameplay. That and Kai Leng. Like in the fact that he actually exists as a character.