Well I've got to be boring and throw my vote (for what that counts for) to Mass Effect 2. I keep hearing complaints about how things don't seem to be making any impact between games, but most of the time it's just because those people overlooked the details. It's a subtle brilliance, assuming they manage to make everything feel worth it by ME3.
As much as I'd like to see Heavy Rain get rewarded for its efforts, I don't think it's GOTY material, just because it's so polarizing in it's entertainment value. I personally loved it, but most of the people I know would dismiss it as a glorified QTE without giving it a chance.
Starcraft 2 was great, but concerning. There's still abusive tactics online, but other than that it's a well done game. Shame they seem to have forgotten how to make a dark storyline though, or make monsters...monsters (that said, I love the Zerg designs, they're just not...Zergy). That and the Prophecies arc felt overwhelmingly cheesy and lore-breaking to me. Many disagree, but ehh...if that's what I can expect from Legacy of the Void, I'll stop at Heart of the Swarm and just read a Protoss fanfic instead. Big issues in my eyes, but the game itself makes for a very enjoyable and well designed experience on its own.
As for Cataclysm...I hear good things though I haven't tried it myself. But as for the new races seeming natural and lore-progressive: I completely disagree, but concede that Burning Crusade was worse.