I broadly agree. I had a flip through the pathfinder skills system and I like what I see so far. BUT so more can be done to fix broken things.
Here's some ideas.
1) Less skills. Roll in more skills like they have done already. Examples as follows;
Animal Handling = Handle Animal, Ride
Appeal = Deception, Intimidate, Diplomacy
Athletics = Acrobatics, Balance, Climb, Jump, Escape Artist, Swim etc
Craft = Craft
Cultural Lore = Knowledge: Geography, Knowledge: History, Knowledge: Nobility, Knowledge: Local
Heal = Heal
Linguistics = Linguistics
Magic Lore = Knowledge: Arcana, Spellcraft, Use Magic Device
Mechanicist = Disable Device, Open Locks, Craft Locks / Traps, Clockworks etc
Mystic Lore = Knowledge: Religion, Knowledge: Planes etc
Natural Lore= Knowledge: Nature, Prof: Farmer, Survival, Weather etc
Perception = Perception
Perform (Choose)= Perform (Disguise is a Perform option)
Profession = Profession
Rock Lore = Knowledge: Dungeoneering, Prof: Mining etc
Sleight = Sleight of Hand
Stealth = Stealth
Trade Lore = Appraise, Prof: Merchant etc
2) Universal skills. No more cross class or class skills. Anyone can access the skill list if they've been using or attempting to use those skills etc. It allows for more rounded characters and people not choosing a class ill suited to their concept solely because it has some skill points in it.
3) Everyone has 4+Int Mod as minimum base skill points. Why have a fighter as a guard when he can't see people? It's not going to overly unbalance things and it means a non human fighter with an Int of 9 is no longer going to have a single skill point he can assign to maybe 8 skills.
4) No more x4 initial skills. With more average skill points, less skills, and no cross class the x4 can be removed and the maths becomes simpler.
5) Create a Skill Focus Feat. The feat allows you to select 3 + Int mod skill focuses. A focus gives a +4 bonus (Insight?) to a subset of a skill eg Perception: Scent or Mechanist = Open Lock. Possibly let someone using a focus take 10. This way player characters can specialise in a broad skill and so can NPCs.
6) Create an NPC class called Citizen (or something like that). Having Commoner and Aristocrat and Expert is dumb. Simply have a typical peasant type a level 1 citizen and a craftsman type a level 3 citizen or something like that. They have poor combat, poor all saves, get 4 skill points (+ Int Mod), but get class abilities of say a Skill Focus feat every three levels. With universal skills a citizen can be readily tailored and skill focussed.