Pathfinder did make a few good changes. However, there are several things that I dislike. Off of the top of my head
Classes: I dislike the majority of Paizo classes. Some of my issues are the same as with default 3e. Others are new to Pathfinder. The only reason that I gave Pathfinder a second look is Owen K.C. Stephens and his Genius Guide to the Talented (X) class books. Outside of Steve Kenson, he is one of the few people that seems able to regularly produce class material for 3e/Pathfinder that I enjoy. So far, he has fixed the Cavalier, Fighter, Monk, and Rogue. I am looking forward the Sorcerer, Oracle and, possibly, several others.
For my tastes, the designers went in the wrong direction with the majority of classes. Cleric, Druid, Sorcerer, Wizard need to be nerfed (for starters, gaining spells at the bard's progression would be my preference). Other issues
1.Barbarian: I am not a fan of barbarian== raging wilderness fighter. Movies, myth and literature do have ragering fighters from urban environments (Barbarian== raging wilderness warrior was an issue in 3e for me as well). Furthermore, in many stories, "barbarian" does not equal rager In 1e, the class had nothing to do with raging, but was a wilderness warrior from a less technological wilderness society. Thankfully, UA had the crafty hunter which was a non-raging/non-spellcasting wilderness warrior that can be an alternative to the rager.
Another thing that I dislike is that unlike 1e, there is no tailoring the barbarian to his home culture/environment. In the culture gave extra proficiencies and bonuses in the home terrain and determined starting weapon proficiencies. The former in 3e could be covered by using the Favored Terrain variant from UA. If a DM is willing to allow alternate ranger fighting styles to be substituted for the archery style- it allowed even more cultural tailoring.
As I understand it, The Genius Guide to the Talented Barbarian from Rogue Genius Games addresses the "urban barbarian" and the cultural aspect. So, I am looking forward to seeing what Owen did in that book.
Another issue that i have is the Barbarian rage powers- especially, the energy powers. The majority of Paizo's powers are a major turn off to me and my friends. It is not what we want in a barbarian class.
2. Bard: Personally, I don't care for the Pathfinder bard. Then again, I don't care for the 3e PHB Bard either. The jack of all trades never did it for me. The only D&D bard that I liked was an alternate bard from Dragon Magazine for 1e. There are, however, a few bard archetypes that I do like.
3. Cleric: The best D&D cleric to me was, hands down, the 2e specialty priests. Any other version that I have seen for D&D/Pathfinder is a just a disappointment. Among my issues
a. Class armor proficiency (even clerics of non-martial deities gain medium and heavy armor and clerics of completely non-martial deities or of, completely, non-martial archetypes still gain Light armor (looking at Pathfinder's Cloistered Cleric in comparison to the 3e Cloistered Cleric from Unearthed Arcana)
b. Spells lists are not tied closely enough to deity domains (an issue with default 3e)
c. channel energy; Why does every cleric get healing or harm if it has nothing to do with their deity's domains?
d. spontaneous casting: same issue with channel energy. The abilities should be based upon the domains of one's deity, in my opinion
e. Clerics not being spontaneous divine casters (Unearthed Arcana). My personal preference is clerics to pray and receive spells as needed. However, I can accept the default method if spells were learned rites since, in some cultures priests. learn secret rites tied to the deity they serve.
f. Planar ally's not limited to being a unique specific creature/avatar or class of creature serving a specific deity.
4. Druid: Personally, for 3e, I dropped the druid in favor of Green Ronin's Shaman (which I find far superior to the playtest version of the Shaman which, in turn, I found better than the Druid Shaman archetypes). Among my issues with the druid
a. Dinosaur animal companions. Giant insect animal companions, goblin dogs, etc. Personally, I would prefer the choices closer to the ranger list
b. Wild shaping into any of the above
c. Changing into elementals, plant creatures
d. immunity to all poisons (for reasons discussed in SKR's Fewer Absolutes)
e. Druids not being spontaneous divine casters (Unearthed Arcana)
5. Monk
a. Purity of Body and Diamond Body granting immunity (for reasons stated in SKR's Fewer Absolutes). I don't mind a big bonus to save, but leaving some chance of failure, in my opinion, is more interesting and allows for things like the character in Crouching Tiger/Hidden Dragon dying of poison.
b. Tongue of Sun and Moon, Empty Body,
c. When I think of monk's using ki, in addition to more rapid strikes, increasing AC and more rapid movement pace, I want:
* making one's self temporarily stronger including for lifting objects
* making the body as hard as steel
* making one's body heavy: rooting one's self to be harder to move, knockback, trip
* making one's body light to leap even greater distances (High Jump) and reduce/negate falling damage being thrown/tripped.
6. Paladin: When I think of "Paladins" channeling faith: I want things like focusing their faith into the "strength of ten men" in addition to laying hands to both heal and remove status effects (e.g., fatigue, blindness) and smiting evil. Off the top of my head, I don't recall a strength of ten men ability. Other issues:
a. immunity to fear and disease (for reasons discussedin SKR's Fewer Absolutes). A chance of failure, again, makes things more interesting (in my opinion). This holds true for the other Paladin abilities listed below that grant immunity
b. Aura of resolve
c. Aura of Justice
d. Channel positive energy
e. Aura of Righteousness: immunity to compulsions
f. spells not gained until 4th level. Personally, I wish there was an option that I preferred to the Warrior of the Holy Light archetype for non-spellcasting paladins. I prefer the non-spellcasting paladin from 3e's Complete Champion. However, if Paladin's are going to cast spells, I would prefer there being a level to do so at first level beginning with 0-level spells.
7. Ranger: my issue is spells not gained until 4th level. I wish there was an option that I preferred to the Skirmisher and Trapper archetypes for non-spellcasting rangers. I prefer the non-spellcasting ranger from Complete Champion.However, if Ranger's are going to cast spells, I would prefer there being a level to do so at first level beginning with 0-level spells.
8. Sorcerer
I like that they get Eschew Materials at level 1. However, I dislike the bloodlines. The nice thing about 3e's heritage feats was that becoming more like the bloodline was optional- in many stories such an ancestry is simply why spells are, innately, cast. I prefer a common 3e rules of choosing a bonus metamagic feats. Furthermore, many of the bonus feats and spells seem arbitrary to me. As a player, I dislike being forced into the designer's choice for many of the class features and ,as a DM, many are just inappropriate for the campaign.
9. Wizards. I like the d6 boost and the arcane bond. however, I want some pre-3e limitations reinstated.
Skills: My issues:
a) I dislike the +3 bonus for taking a rank in class skills- especially after first level.
b) I dislike Pathfinder's rank limit by level
c) I prefer 3e's x4 skill points at first level and bonus simply determined by ranks purchased
d) Clerics, Fighters, Paladins, and Sorcerers still only receiving 2+INT skill points per level.
Feats
I dislike the names for many of the combat feats. Not everyone runs Golorian or uses everything from the Monster Manual. For this reason, I want more generic names not Gorgon's Fist or Medusa's Wrath as a home brew campaign setting may not have Gorgon's or Medusa. Generic names (e.g., staggering strike) don't require telling players to rename something and hope they remember. Plus, Gorgon's strike and Medusa's Wrath feats have nothing that resembles a Gorgon or Medusa's attack.
Combat:
Martial types not making full attacks as standard action.
I have more issues with Pathfinder and may list them later. However, as for running it, I, probably, will not consider doing so until Owen finishes covering the core classes in his Genius Guide to the Talented (X) line of books. Then again, I may just use the books for 3e and bring in a few other things (e.g., some Pathfinder spell changes) into my house ruled 3e.