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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That there wasn't a feel of exploration like ME1 & ME2 had.