and it's not unusual to have the main char on the cover for an fps
Not unusual sure, but not an image or a character I connect to the game in any way. A lot of the other examples you posted are recogniseable parts of the game, or recogniseable stylistically as part of the game. Even though we know Booker is the main character, he hasn't show up in any trailers, or any clips, or any promotional stuff and hes generic looking enough that hes not immediately recogniseable as a distinctive part of the game (such as is the case with the Crysis Nanosuit or the dude from Dishonored).
Not really a big deal, I don't buy games based on their cover art, I just found it odd that they wouldn't go with something more distinctive and something that is known to the fans and more recogniseable as being Bioshock. I mean, in the first game they didn't stick the main character on the cover, they stuck a Big Daddy on the cover, cos that was the instantly recogniseable hook of the game, would have expected something similar here.