Yeah, I'm surprised too. I'm thinking that they chose the GOTY nominees before Halo 4 entered the review stage though, otherwise it would be an obvious choice.
...Then again, there are a couple other games I would have like to've seen on there, so it's always a clash of interests. Oh, and 343i deserves the Best Studio win. Gearbox is fantastic, TellTale is one of the most admirable devs out there, and Arkane has busted onto the scene in definitive style, but 343 Industries produced a resounding success in the face of a nearly immeasurable challenge, establishing themselves as the new hyper-competent holders of a legendary franchise, tasked with making sure it remains so. Through that, they'd had to (and more than did) earn the respect and trust of diehard long-time fans of the franchise. If that doesn't make them deserving of that award... I don't wanna know what does.