Well, to be fair, you see everything through rose colored glasses when you're a child . Truth be told however, I really didn't find the' 03 turtles so drastically different from the original 1990 film or even the cartoon. I mean, its not like comparing Batman Robin to The Dark Knight.
Die hard TMNT fans may disagree ,but as someone without deep loyality to either version , I gotta say , there really isn't that great a difference beyond the loook and the times they were made in.
The guys have pretty much been the same since they appeared on TV in the 80's and i've yet to see any TV or movie version which has really done a 180 on the characters or tone. And to be fair to Bay, his description, aside from the alien idea, sounds pretty close to what the characters are so I doubt he's gonna do anything radical in terms of that aspect.