I've got the PS2 version and am happy with it. I've only had time to play a couple of games and haven't looked at the dynasty mode yet. A few things are different - for one you can not throw accurately on the run (at least not on Heisman with a low 80's QB). When you call timeout you get a brief scouting report on your opponents tendencies. I like the changes so far.
If you are like me and not going to bite the bullet and buy a PS3 yet it's worth it.