My two cents are that you may have a buggy installation of some sort.
When I first got my HTC Desire HD it was slick and snappy. When it was upgraded from Froyo to Gingerbread it became laggy at times and behaved in ways that erred with me. Even factory resets didn't help. So when ICS wasn't going to be available for it I decided to root and flash a different ROM. Now it's slick and super snappy. As part of flashing a custom rom the phone recieved a full wipe so anything pre-existing that could have been causing problems went away with the wipe. You might say that the custom rom is better and that's why it has improved but I'm pretty sure that if I had flashed it with the stock rom for it I would see it become snappy again too.