The Pathfinder skill system remains relatively unchanged with a few additions to accommodate extra skills from D&D 3.5:

• Concentration returns as a skill (as it was in D&D 3.5), but characters can still choose to make Concentration checks as in Pathfinder if they prefer.  The primary difference is that the Concentration skill now incorporates many other similar skills from D&D 3.5, including Autohypnosis, Control Shape, Hypnosis, Iaijutsu Focus, and Lucid Dreaming (and perhaps others).  The ability score applied to Concentration checks changes to match its use.  For example, you'd use Charisma for Iaijutsu Focus checks or Wisdom for Lucid Dreaming.
• D&D 3.5's Truespeak skill is now part of the Linguistics skill.
• D&D 3.5's Knowledge (tactics) is folded into Knowledge (martial) (from Path of War).  Similarly, Battle (from Rokugan), Martial Lore (from Tome of Battle), and Knowledge (warcraft) are now part of that skill.  Knowledge (ancient history) is simply part of Knowledge (history).
• Several Rokugan skills have been incorporated into other skills:
  • Knowledge (ancestors) => Knowledge (nobility / history)
  • Knowledge (barbarian lore) => Knowledge (local)
  • Knowledge (elements) => Knowledge (arcana)
  • Knowledge (etiquette) => Knowledge (nobility)
  • Knowledge (fortunes) => Knowledge (planes)
  • Knowledge (law) => Knowledge (nobility)
  • Knowledge (maho) => Knowledge (arcana)
  • Knowledge (research) => Knowledge (local)
  • Knowledge (shadowlands) => Knowledge (planes)
  • Knowledge (shintao) => Knowledge (religion)
  • Knowledge (spirit realm) => Knowledge (planes)
  • Knowledge (spirits) => Knowledge (planes)
  • Mimic => Linguistics
  • Tea Ceremony => Perform (ceremony)
• The Games category of skills is available as in the Rokugan Campaign Setting.  These are background skills.  The Ledge board game primarily uses Wisdom.
• Ravenloft has a few skills requiring conversion as well:
  • Monster Lore => appropriate Knowledges
  • Knowledge (ravenloft) => Knowledge (planes)