Bad story, glitches up the wazoo, the Riddler stuff was changed be so ridiculously time-wasting and obnoxious, and it doesn't have nearly as great a flow as the original had. Just goes to show bigger isn't always better.
Also Metroid Prime 2. Not a bad game by any stretch of the imagination, in fact it's still very good, but it's just not as good as the original.
I'm somewhat surprised considering this was a strong game of the year contender when it came out but it seems to consistently be brought up in regards to the original question.
Personally speaking I thought it was a great game but I did like Asylum better. I felt City "lost" something in terms of it's flow by changing the formula from the first game and becoming more "open world."
It's funny but I thought I was the only one who thought the original was better, especially when you consider all the praise City was getting when it was released.
-STILL GOOD BUT... NINJA APPROVED-