Paizo is not responsible for the high-level problems of 3.x- that is a built-in fault of the system.
However, IMO Paizo is responsible for escalating the arms race in their modules and materials, and for bad encounter design. I believe from previous comments I've seen on ENWorld and the Paizo board its even been publicly stated by Paizo that they assume all PCs should be optomized who play their adventures, and that many of the encounters are designed to be very difficult/meat-grinders. I know after we played about 60% through Age of Worms, we quit playing 3.x althogether due to the royal PITA running and playing a game had become, and went on to other systems until 4e came out. I loved the concepts and story for AoW, but the implementation was terrible IMO.
Ourph made a very good point about the power escalation in Paizo products, and their use of custom monsters. Personally, I like custom monsters- it keeps PCs on their toes. While many of the Paizo monsters are very cool conceptually, many of them seem overdesigned, such that they are not on par with monsters from the MM of the same CR, which makes it hard for a DM to know what he's getting himself into with Paizo materials. This is a trend I've noticied in Paizo stuff from the start- they tend to increase the power such that you're playing "D&D with the power level cranked up to 17". Having seen their APs so far and the Pathfinder Beta ruleset, it hasn't eased my reservations with Paizo, and it seems to be a chronic problem with them IMO.