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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Kasumi's Stolen Memories was my favorite DLC besides Lair of the Shadow Broker. As for a disappointment, that would be that Banshees, Brutes, ATLAS's, and the Rachni are just glorified bullet sponges. I love the game and its entire series none-the-less.