Very few things irked me about the ME games. They are such amazing experiences....
Randomly roving about the lifeless planets of ME1 was a bit of a drag; I was not happy to see the Mako is back, but hopefully the experience won't be as painful this time.
Agree on the minigames, ick.
Planet scanning; it was the worst in ME2, but in general, I don't like it. I really don't like that it's something you can't skip, unless you're fine with, you know, your character DYING.
Going from "overheating" to "you ran out of bullets lol" Boo.
Very little customization in the CC. For a BroShep you pretty much gotta make a military meathead. Which, okay, get it, works with the story. But it's a small thing. Hopefully "Ryder" (is that still his/her projected name?) will have more options.