Origins' story is overrated? Lol where? Is the most underrated of the 3, yet, probably the second best.
Joker's story is fantastic, the way Joker met Batman was like twisted love at first sight, it was perfect, what's also perfect is the representation of a young, rougher, inexperienced Batman, they nailed that one.
How Batman and Gordon's relationship came to be is also top notch, you get some character development and interactions that you just don't get in any of the other 2 games, Barbara's bits were also great.
A bunch of Assassins are trying to kill Batman cause he's a problem for the mob, what's not to like?
When you find out Bane discovered the batcave and Alfred's not responding, you actually feel the urgency, I didn't feel that in City near the end.
If the gameplay didn't have so many bugs on the PC version it would probably be considered the best of the franchise, yeah it took everything City did, but what did you expect? It DID expand on some things mainly in the fights, city navigation, etc etc, added a couple enemies that made Origins fights the most fun of the 3 games, the martial artist enemy type made them a lot more varied.
And the design of the characters was probably the best of the 3 games.