I'd be willing to bet that a major part as to why a Harry Potter cartoon hasn't been made yet is because
a) The seventh book was only released last year. Making any sort of cartoon before that - be it a prequel, direct adaptation, or sequel - would be liable to leaving out certain plot elements or creating plot holes, unless the producers were willing to go the Fullmetal Alchemist route and have it diverge from the main plotline (which Rowling would NEVER allow)
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b) Warner Bros. maintains complete control over the property, and probably figure having the ongoing movie series and a TV series at the same time would saturate the property.
On a similar note I remember Steven Spielberg had wanted to direct the first Harry Potter film and have it be animated with Haley Joel Osmont as the voice of Harry. Obviously it never came to pass, mainly because of J.K. Rowling's objection to having an American boy portraying a British character like Harry (further trivia: Liam Aiken was scheduled to play Harry in the original Philosopher's Stone film, however, as he was only half-British, he was dropped from the project in favor of Daniel Radcliffe).
I'm having a difficult time deciding where I would want a Harry Potter series to go. Perhaps, like I said, a direct sequel about Harry's post-Hogwarts life, except the lack of details provided by Rowling would require a more creative effort on the part of the animators themselves. A direct adaptation of the books? I'd kind of like this actually, if it would streamline the series as successfully as The Spectacular Spider-Man has. I actually think this would be the best route to take a series, as I assume it'd be launched well after the film series is ended.