Hey there,
First, I'd just like to say thank you to Paizo for providing a 3.5ish alternative to 4e. I've liked what I've seen so far from the Pathfinder RPG Alphas. Keep up the good work guys.
With regard to skills, I have a suggestion to allow players to customize their classes a little more. Allow a player to pick a number of skills (player's choice) to always be treated as class skills, equal to their intelligence modifier. So, if their character has an Intelligence of 16, the player can pick 3 skills of their choice that are always treated as class skills. Even if the character multi-classes, these three skills will always be treated as class skills. This will have a couple of effects. First, Intelligence will no longer be thought of as a "dump stat" for the more martial classes. Secondly, it will help characters differentiate themselves from each other, even if they are from the same class. It won't give a character any more actual skill points, but it will give them more choice of what to put their points into if they invest in intelligence.
Half-Elves have now become a much more viable option for players, beyond just the fluff they added in standard 3.5. To tweak this a little further, I suggest that they give them two options, that must be determined during character generation, which reflects their upbringing. If the Half-Elf is raised in a Human community, they are proficient in a martial weapon of their choice (or an exotic weapon if they already have martial weapon proficiency). If raised in an Elven community, they Half-Elf treats all weapons with the word "Elven" in their name as martial weapons. Gives a little bit of crunch, but also distinguishes Half-Elves raised by Humans from those raised by Elves.
Just a couple of suggestions for the designers (and the community in general) to mull over and discuss.