I liked the "human-into-a-rat" version because it was just easier to believe in a way and seemed a little less ridiculous. I remember when I was 8 and saw the first movie in theatres with my older sister and my cousin; none of us had any idea about the Mirage comics, only the old cartoon, so we had no idea about Splinter's origin as a rat. We must not have been the only ones; when they showed Splinter as a rat doing kicks and stuff in his cage, almost the entire theatre erupted with laughter and a few "oh come ON"s as if it were the most ridiculous thing ever, and my cousin gave me a look like she wanted to kill me for dragging her to this movie. So I admit I never liked that version of the origin from the start.
I never heard anything about Splinter not being a normal rat until like today or when someone mentioned it like two days ago in another thread; where'd you hear that? Was it ever actually explained that he was already undergoing some sort of mutation, or is it just assumed?
I'unno, as I've said before, I know the entire thing about the TMNT is really farfetched in general, but for some reason I can buy everything EXCEPT a pet rat doing martial arts moves in its cage.

So I like the other origin better.