Just a quick list of my biggest PF issues. I might expand it more if I have time.
1. Doing the impossible and making the caster/martial imbalance even worse than 3.x.
a.Partially from new better spells(Fickle Winds is Wind Wall with all of the downsides removed, Bestow Grace of the Champion is basically a "become Gestalt Paladin" on demand, Wizards can cast out of banned schools and get hilariously overpowered class abilities[biggest gripe being Divination Wizards get surprise immunity at level 1, and a scaling level bonus to their initiative rolls]), class abilities as mentioned above, and new casters toys(UMD for every caster, traits that give too many good caster-related perks[+2 to spell DCs 1/day, making UMD key off Int], and Paragon Surge completely breaks Oracles by letting them access their entire spell list which includes Bestow Grace of the Champion on a CHA fullcaster)
b.Nerfing martials(Rogues lost methods to make enemies flatfooted, Tumble got completely gutted, and can't sneak attack with splash weapons, and get bullied out of the skill monkey role by casters with INT giving retroactive skill points). Trap options everywhere(The Monk class, many feats, and the crossbow in particular. Equally optimized, a crossbow bolt does less damage than throwing the crossbow itself at the target or throwing water balloons at the target)
2. Going back to trap options. Too many things sound good(like the aforementioned crossbows, as well as pretty much any maneuver), but it pretty much takes most, if not all, of your feats to make it even worthwhile and by that point the casters have hit their "A God Am I" phase. And with the removal of the flaw system, Martial classes end up with less feats than their 3.x counterparts(a PF character doesn't catch up in feats to a 3.x character with 2 flaws until level 15)...which is worsened when you remember that Pathfinder added/extended a lot of feat chains to get to the same effectiveness a 3/x character would(so in all, a PF character has less feats choices, but needs more feats to match a 3.x character). Casters, of course, don't feel this as badly, especially with new caster feats(helloo Dazing metamagic, giving me a Save or Suck spell that lets me hit any save).
3. Since I mentioned maneuvers, one thing I will say Paizo did right was cleaning up 3.x's maneuver system. Instead of...whatever monstrosity 3.x had, we now have CMB vs CMD for maneuvers. Nice.....except this system HEAVILY favors monsters over players(since the system is based on STR, DEX, and size modifiers, something monsters will typically have metric tons of in spades), and even optimizing maneuvers makes them nearly impossible to use against anything that would be any threat by the time you hit level 10 or so(and that's even before factoring in the number of monsters that are effectively immune to a given maneuver).
Not to say I don't like Pathfinder. I love how they fixed up the Paladin(Smites per enemy instead of per attack, something I hate the Holy Gun archetype for bringing back), some of the new classes are interesting(despite the Summoner being broken, Synthesist archetype not quite as much but still overbearing), and the archetype system is fun.
And I'll close with a personal gripe.
Where is my Blue Mage-eqsue class? I know this is more difficult in Pathfinder since unique monster abilities are fairly rare(since most use Spell-Like Abilities you could find on someone's class list), but still. I will give a nod to the Taskshaper for being close however, but it's third-party so I won't credit Paizo for it*shaking fist*