My experience with Pathfinder's skill system has been that it reduced the complexity and book-keeping of the 3.5 skill process by removing cross-class half-point buys, and made it easier for players to focus their skills on what was really reflective of their characters. In actual play its proven to have no real functional difference, except that there are fewer gimped skills popping up.
I was a king of gimped skills when I played 3.5, never did I have a character who wasn't a jack of all trades and master of none, capable of rolling and failing almost all skill checks called for... =)
Anyway, I had one player to date who initially was discontent with the Pathfinder skill system. After a couple sessions he decided it was smoother and ultimately more flexible, although it did requrie thinking about what constitutes a focused vs. tertiary skill a bit differently.
The only gripe I have with Pathfinder's skills, personally, is the absence of Streetwise. Why is it missing? It's a skill I regularly call on in other editions.