I didn't have a problem either except for one scene: his takeover of the stock exchange. That's was it. However, there is an obvious break in the effect during the first fight scene - Hardy's natural voice came through loud and clear.
I, too, also noticed that Gotham was obviously Manhattan Island this time. At least in the first film, there was some attempt to hide it. My inner geek was a little peeved at DC for having fictionalized the names of cities in the DCU in a manner Marvel never has.