Well. I'm not saying the story was bad or anything. It was solid writing. But I can't say I exactly felt mind blown by it either. It was super heroes battling super villains, doing their usual thing. And the plot twist towards the end when you found out who the real mastermind behind it all was felt kind of... pointless. It's also a bit hard to feel something when you see a comic book character die, because you know they're probably gonna show up later one way or another anyway. And of course, every woman in the game/batman universe is super sexy and flirting with batman. And yeah. I agree about the aesthetics. But it also managed to look really good at the same time, so... :)
I didn't play Arkham Asylum. But I though Arkham City had an amazing story. This isn't saying much but I thought it blew any other comic based video game out of the water and far surpassed most AAA games in terms of story telling. I'll go even further and say it was even better than Dark Knight Rises. I thought the aesthetics were a little tacky, but that's a matter of taste.