Pathfinder Skills: The Good
Perception: The single best improvement to the D20 skill system is without a doubt the elimination of Listen, Spot and Search and the combining of these skills into Perception, the replacement skill. This is just a time saver and who really cares, in a RPG, whether an observation came from your ears, your eyes or your underwear? No one cares whether your eyes are better than your ears either. The skill description even mentions that all five senses are involved (hell, I would even have gone so far as to mention that "sixth sense") so not only is it a replacement, it takes senses into account that weren't really taken into account before. Perception is a more complete way of seeing (pardon the pun) if your character notices something amiss.
(Per Parte the Firste, I have to nod to 4E because it too boiled Listen, Search and Spot down to Perception. Yes, a nod to 4E. Try not to faint. I still don't know what "Insight" is, other than something your players should actually have rather than roll upon.)
Linguistics: Spending a skill point in Linguistics does 2 things: it buys you a rank in overall linguistic knowledge and you learn a new language. This is good because you're now not expected to cram the 23 dialects of Elven your character speaks into the skills table on a front sheet. Unfortunately, there is a minor bad (see Parte the Fourthe).
Points: If you put a rank into a class skill, you get a +3 bonus to that skill (bonus, not additional points). This replaces the x4 multiplier all characters at first level received. This is genius because it eliminates the distinction between building a 1st level character or a 10th level character, from a skills perspective. The skill point distribution works out the same if you select class skills and...
Choose Wisely: ...so, the other good thing about this is that it drives players toward better skill point decision-making. Instead of getting a lump of skill points at 1st level and spending them like an idiot on cross-class skills a character's just not going to be good at, in part or whole, Pathfinder encourages players to spend in their skill area without dictating it as a must. Players that stupidly continue to spend skill points on cross-class skills they suck at (particularly if their ability score is also low... which is a downgrade from "idiot" to "retard") WILL lose the equivalent of skill points (remember it's a bonus) when compared to D&D 3.5, but frankly, they get what the deserve if they do. Your fighter/sorcerer doesn't need underwater basket weaving, damnit!
Less Is More: Because there are less skills (per Parte the Firste, D&D 3.0 = 42 skills, D&D 3.5 = 36 skills, PFRPG = 26 skills, 4E = who cares?) one might argue that players get more skill points, though I've read at least one blog post complaining that you still don't get enough. That just doesn't seem so to me unless you make idiotic skill decisions (see above). The elimination or combination of 10 skills, for a net balance of 26, seems to mean that the skill points you do get will see more efficient use.