On the other hand, it's not like Supergirl didn't also have a myriad of problems of her own before the 2000's version: She's made of protoplasm and from a pocket universe, she's an Earth woman, she's an Earth angel etc. I don't even remember how it ended.
But in the end, all those weird choices were taken because they really wanted to make Superman the very last kryptonian. Considering how things are currently that wasn't really a good decision. But in the end, I can sort of see why it was done what was done.
And back to Ultimate Spider-Man I think that would have been better: Whatever changes are made, at least make them for a purpose, not for the sake of just being different. Doubly considering how much it seemed to follow the original Spider-Man anyway.