And using the genetic experiments angle didn't do much harm to the Spider-Man franchise. We've seen hundreds of changes to character back stories in comic books. I don't see how them being test subjects (something the IDW series has done to a lesser degree) has really changed the tone.
Okay, so then why change it? It's change just for the sake of I'm-Michael-Bay-and-I-don't-have-to-give-a-f__k-about-the-source-material.
I'm sure there could be a great show about an alien guy with superpowers named Bruce Wayne who dresses up as a bat and fights crime. But it ain't Batman anymore.
It changes the tone when the turtles were intentionally created in any way. They were supposed to be mutant accidents. Look at the 2nd movie in the 1990s, where one of them was even having an existential crisis when he finds out the true circumstances of their creation. It was a huge part of the franchise that these were TURTLES - seemingly the least-cool animal you could think of for an action hero - living in a SEWER - the least cool place in NYC to dwell - and just trying to carve out an existence & survive. They were short, ugly, uncool, dirty . . . basically the antithesis of all that was badass heroes in the 1980s. And their father/mentor was big overgrown mutated rat.
There was a time when TMNT was not a household known thing.
THIS was how you reacted to the idea of TMNT when first introduced to it. I'm old enough to remember. That's how it felt when you first saw the ninja turtles, and this was how you reacted to the origin story. Just like how it should still be affecting the fictional characters, both the mutants and the humans they encounter, in the fictional world where TMNT is still not a household thing.
But now they are something totally different in this new movie.
Why?
I dunno. Just because:
"I'm Michael Bay and I don't have to give a f__k about the source material. I'm a hack producer who can't make a good movie on my own but they know I can produce products. So I keep on getting stuck rehashing these idiotic 1980s toy cartoons, which I hate but I do it for the money. So f__k taking any creative risk, I'm just gonna do what has already worked recently. I had planned on rehashing my own Transformers backstory with these green critters, but too many people bitched when rumors of it leaked 2 years ago. So we'll just copy Spider-Man this time instead."
TMNT didn't deserve this. It has a multi-generational fanbase that would have supported a non-insulting reboot and happily introduced it to their kids anew.