Origins has the best story of the three, though. The characterizations and character designs are better, and Batman is Batman. He's not on a constant fetch quest, but is actually going out there and doing detective work. I found myself appreciating the story alot more than I did in the first two games.
That being said, the technical flaws and glitches and game breaking bugs people have encountered are far too glaring to simply ignore. I feel like had the game been much tighter and polished people would have been far more receptive. Hell, even the multiplayer (which was actually kind of fun) was horribly broken and a chore to partake in.