I don't agree with dismissing Cave Johnson. He's one of the central characters in Portal 2. Like Jeff said, a good character really isn't more than voice acting and writing. He's long dead by the events of the game, but he still gets a satisfying story arc, his dialog is hilarious and J.K. nails the part.
I agree, but I think they were just looking for a reason to only have one Portal 2 nomination in a category with plenty of worthy mentions.