>>149059594
There could be a lot of reasons why but what I suspect are a combination of these two:
1. Canonically, Shredder was an important character for the origin story but still a minor character because he died in the first issue, with all other appearances being a homunculus made of worms. Once the canon stories had been adapted, it was deemed safe to reinterpret him because he had already done everything he did in canon.
2. As originally presented, Shredder is really nothing more than a glorified Yakuza dude with martial arts training. While that is not a bad villain, it's also fairly small potatoes in the grand scheme. If you are to present him as the true main villain in a world full of aliens, robots, demons, time travellers and whatever other comic book insanity you can think of, he needs to be a credible threat even when those elements are in place. So it makes sense to change him from a normal-ish criminal to an intergalactic threat.
It's not just the 2003 show that does stuff like this to him. The live-action and 2012 adaptations may start out depicting him a normal human but he does still end up juicing ooze to become more powerful there. In IDW he's the reanimated avatar of a destruction god and in Rise he's a ghost bonded to armor. I would not be surprised if Mutant Mayhem 2 reveals him to also be something crazy like that.
