If you pay attention to people defending Bay's words, and saying that TMNT should be aliens, you'll probably see a quote like this:
"All of you fanboys aren't seeing the big picture: maybe Bay changed the back stories because he has no real passion for the original and wanted to make it his own so it could be the best it could be!"
First of all, supposedly the production team of any adaptation are all fans of the material they're adapting. If the above quote was true, it would prove that directors and producers are horrible liars (which, they probably are). But even so, why would you want to adapt something to the screen that you're not a fan of? Of course the easy answer is, "For money", but TMNT is a little specific of a choice, mostly because it hasn't made any sort of money in a few years (which was probably pennies when measured against its past success).
If you're going to bank on nostalgia, why change anything? Point to five good movies where a drastic change in what the original property was, yielded a good movie specifically because of that change. You probably can't; and yet while you can't, writers, directors and producers still think it's appropriate to change stuff, arguing with the logical fallacy that a version taken strictly from the source would not turn out as good as it could.
It also enforces that horrible stereotype that if you have any kind of passion in something fictional, that you're automatically a basement dwelling fanboy. "Why do you care if they change anything? Are you a nerd?" You know, the members of the Wu-Tang Clan are huge comic book fans; do they look like basement-dwelling fanboys? And if you thought they were, would you honestly say it to their faces?
On the other side of the coin, minor change is to be expected in adaptations for various reasons. That kind of change just usually ends up being more noteworthy than actually important. However, that doesn't warrant huge change just for the sake of change, or because one person wasn't passionate enough.
You're getting paid to make a movie; that should be passion enough to do it right.