Personally, I'd keep the skill list pretty much as it is, but divide it into some categories (mere examples, which could be changed to anything): athletic skills (Acrobatics, Climb, Swim, etc.), lore skills (Knowledges, maybe Spellcraft, etc.), professional skills (Craft, Profession), social skills (Bluff, Diplomacy, Sense Motive, etc.), utility skills (Heal, Survival, etc.), and so on.Theny, each class and creature type would gain a number of skill points for each category.
Fighter would gain a good amount of athletics points, a decent amount of utility points, and low lore, social, and anything else.
Wizard would gain high lore points and low anything else.
Things like these.
So you can dedicate to spending your points on each category without worrying too much that your character needs a social skill to back up his background but has low points and you can't forego other skills.
Without giving too many points to spend boundlessly at the same time.
I like this idea, but working out the numbers with points to spend in each category would be cumbersome to say the least. Don't have a solution though.