I have seen no indication that they are gone, but I can hope.
More often than not, I found them completely illogical in that many of them (Spot, Listen, Heal, most of the atheltic skills, etc) didn't have much to do with the classes. Why does a pickpocket have an easier time learning to play the flute than a warrior? Why does a thief have a better spot skill than a guard? Some of them (chiefly Use Magic Device and maybe Spellcraft) would have been better as class abilities rather than skills, and I'm not completely sure what I would do with the stealth skills (probably now one skill), because these really should be specific to some classes. Other than that, I want class skills gone.