If Kristin dos Santos is to be believed, it was Kristen Bell who wanted to leave the show.
Still, KB's utter on-the-record silence re: how she felt about the way she was shown the door is deafening. It may or may not lend credence to the belief that something happened near the end that really soured her on continuing with the show, even if her movie schedule had allowed her to come back sometime in season 4. Namely BTW, Sylar, here's your son.
But with ACAPD getting mixed media reviews at best, and ennui setting in (both Entertainment Weekly and the Philly Daily News declined to review the episode, USA Today devoting only a 2-sentence review in their what to watch column, and Newark Star-Ledger critic Alan Sepinwall basically saying 'no mas', I'm done with the show), I don't think they'll get a full season 4 pickup if things don't improve. I believe it'll be a 13 episode deal, with the back 9 or 10 hinging on how well the first set of season 4 episodes do. Just my opinion.