@Blinkin: That's pretty much my assessment of Pathfinder too. It fixed some things (and for those things that it fixed, I'd be thrilled to use the PF rule rather than the 3.5 rule) and the creators left some things alone that I think needed fixing. (Example, I HATE vampire spawn because they only exist for a mechanics reason, not a story reason.)
@kongming: I might be persuaded to do allow the Unarmored Defense Bonus, just as I have traits and flaws (also from UA, if I recall correctly). Let me take a look at it.
@Xanatos: Well, with the caveat that the adventure will go for the most part in the direction the players take it, I don't expect there to be too much call for Appraise, Handle Animal, Intimidate (until I fix it, a least; it's broken), or Survival. As for Gather Information, I'd rather see that handled in-character rather than with a roll. That may be all I can firmly say probably won't be used.
As for what will be very useful, Bluff is always great, Concentration if you're a caster (though keep off the front lines and you don't need it to be too high), Diplomacy is good, Listen & Spot will keep you alive, Knowledge is fantastic, Search is key (unless you think you'll always have time to take 20), Swim just depends on whether the adventures plan on going on a nautical adventure, though having a point or two in it could keep you from drowning.
Is that what you were looking for? The other skills will probably just be as useful as the adventurers want to make them.