I seem to recall someone at Paizo (Erik Mona?) stating flat out that their intention was always to support "the current version of D&D" if possible. However the commercial realities around having to keep content flowing to pay the bills, and the lack of information from WotC around 3rd party publishing meant they had to pursue other alternatives.
Edit: Can't seem to locate the article I'm thinking of now, but here are a couple of quotes from
another article:
"[WotC] made all sorts of assurances to the community of third-party developers about how open the new game would be, how they planned to share the rules early with key publishers, and how we could all get on board with supporting the new edition," Mona said. "But something happened behind the scenes over there at about that time, and a licensing agreement that had been touted as a 'more open than ever' failed to materialize."
"All of a sudden our subscribers started begging us not to convert to the new game system," Mona said. "The fact that many members of our editorial staff shared some of these concerns underscored our uneasiness with the dragged out licensing situation. We finally made the decision that if we weren't able to support the game at launch, we might as well not bother supporting it at all. So we decided to stick with [D&D] 3.5."