I wouldn't mind seeing a Harry Potter animated series. It could cover some of the comic events that don't take place in each movie. I would love seeing Peeves, and I an only imagine how it'd be having Harry sneak around Hogwarts with Snape in pursuit, uch like he is on the video games.
With that being said though, unless they did events that take place that aren't in the movies, then no, I wouldn't want a seperate story. I've always thought Harry would work better as an animated series than the movies though.