As a child of the 80's I grew up watching the original series. I also loved the movies, and at that age I was able to distinguish that the stories of the sets of Turtles were different, and both differed from the comic books quite a bit.
Then in 2003 TMNT started and I wanted NOTHING to do with it. They were not the same turtles I knew and loved, but the series followed the comic books more.
It wasn't until
Turtles Forever, where three sets of turtles(prime, 80's, 2003) came together that I loosened up a bit on how essentially there are multiple versions of our favorite turtles.
Of course the 80's turtles cracking jokes was the best part.
Of course, I think its a huge cope out when someone goes the alien/aliens did it route, and no matter what it will always feel weird but really, Its not worth getting your panties in a twist about it especially with series like this that was started as a satirical comic book that very quickly expanded.
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On the subject of messing with the "canon", It's actually the co creator of the original comic book series Peter Laird that is telling everyone to "take a chill pill" and "relax" NOT Micheal Bay. Any decision on "canon" have been decided by this guy, and he seems to be on board. Hell, in the last volume of the comics he made them in their thirties.
Yeah, it's asinine, but let's get over it and accept it already. Maybe the movie after this one will be about the turtles in their 30's, who knows....