So anyways, here's the problems with skills:
Most skills are worthless. This can either be because the skills do nothing that you care about, or because minimal or no investment does everything that matters, and there's no higher level abilities with that skill worth taking. An example of the former is Use Rope. An example of the latter is Survival.
Skills have Planned Obsolescence. For examples, see any movement skill not named Tumble.
Skills are narrow. This last one is the biggest.
Consider if you will a Rogue. He has 8 + Int skill points, which is of course rather high. He wants to scout, which is a fairly typical thing for a Rogue. Now, let's ignore the whole automatic annihilation of scouts thing, and instead focus on the cost. Well, obviously he needs to be able to conceal himself, and he needs to be able to detect those concealing himself from him. And he needs to be able to do the usual Rogue stuff, both because it's typical in general, and because that's likely to come up while sneaking around. Here's the problem. Just doing these three basic things cost him 7 points a level. And he doesn't even do any of them that well. So if say, you want to also be able to talk to people, or make yourself look like something else, or play with your wands, or break into second story buildings? Fuck you.
So here's this so called skill monkey, who can barely fucking do anything with his skills. That's the biggest problem, both in that the guy who specializes in something ends up walking CAP bait because of it, and because it means the normal characters do even less with them.
And because of this, even the handful of skills that don't automatically fail still do, simply because they are so damn narrow. It is such that there's quite a few classes out there that could not even write their skills down at all, and it'd barely make any difference. Both because of the narrowness, and because most of it goes towards taxes, anyways. As opposed to skills you actually want to take. For example, the Cleric has Concentration, and Spellcraft, and unless he has an unusually high Int, or is human, or Cloistered that is literally all he gets. Now you might be tempted to say something to the effect of "He's a Cleric, he doesn't need any more power." While perhaps true, the Cleric is hardly the only 2 + Int skills class, and in any case the point is that the Cleric literally does not interact with the skill system at all beyond paying taxes.
So, solutions stolen from my own house rules thread:
No one has less than 4 + Int skills. Anyone that would get 2 + Int instead gets 4 + Int.
Start fusing similar skills together. For the full list, see the house rule thread.
Now instead of Mr. Walking Corpse... I mean Scout, spending 7 skill points a level to do 3 basic things, he spends... 4. Perception, Stealth, Search, Disable Device. And still does those things. So now he can talk to people (1 skill) and make himself look like someone else (1 skill), and play with his wands (1 skill) and break into second story buildings (1 skill) and if human and/or Int > 10, he can get more. Yay for actually being able to use skills to do stuff!
Of course, the bad skills are still bad, but fundamental flaws are fundamental.