For me personally...
Alternate class features (I think those are the 'archetypes'?) don't even seem to be close to being balanced against each other when it comes to some of the classes. "Hmm... I can gain a few extra feats or be able to do a full attack action after moving; I wonder what I'll pick..."
Maybe it's just me and the people I know, but the Summoner has caused problems in virtually every game of Pathfinder I've been in. (To be fair, similar issues come up when playing 3.5 and makes a character based around summoning.)
The d20... I know that sounds weird, but, as time goes on, my dislike for the d20 grows. I'd much rather see it replaced by multiple dice such as 2d10; heck, I'd even accept something weird like 1d12 + 1d8. Sometimes the swinginess of the d20 can be exciting and cool, but most of the time I feel like it means -at any given time- I have just as much chance to completely suck at trying to do something my character has trained his whole life to do as I have a chance to do something useful. In some cases; if playing with a DM who uses critical fumbles, I suddenly have an increased chance of killing myself as I become more skilled because I gain multiple attacks and more d20 rolls. A little bit of a bell curve would be nice. (On a side note, I think 5E's 'bounded accuracy' is attempting to address some of the issues I have with the d20 and how D&D does things, but 'bounded accuracy' hasn't at all played out in actual play the way I thought it would.)
In spite of some new abilities, there are times when I feel like the PF Bard is worse than the 3.5 Bard.
Just for a counterbalance; things about Pathfinder I like...
Much better way of handling Favored Classes.
Capstone abilities for classes
The artwork; goblins in particular
Getting rid of 'dead levels' as much as possible.