If I really only had to choose one,
Dark Souls
There weren't any good story based games that come to mind for 2011, but I might be forgetting something...
Don't think so though. Except Corpse Party, which is awesome and a definite honorable mention, but I wasn't satisfied with it enough to allow it to surpass Dark Souls.
Skyrim was fun and interesting, and large. But Dark Souls' gameplay and difficulty easily skwered Skyrim. I loved the crap out of it.
Saints Row the third...eh there's a lot of honorable mentions, but basically the only game I was excited for, got at launch, and was giddy like a school girl for months for, was Dark Souls
and before I post I remember, Fate/Extra.
That was also an awesome game, with an interesting story. Mostly because the Fate universe itself is just fucking awesome. But still, story didn't compensate enough to make it surpass Dark Souls.