In 3E, I can take a bunch of feats in order to be really good at tripping people with a spiked chain. Figuring the most optimal combination of feats (and skills) at the very least takes a few hours. I have to make sure I understand what the heck my characters abilities are, how they interact, and when and how to best use them. Once I do all that, is my character unique? Not unless you think that tripping people with a spiked-chain is unique. No, after a couple hours of effort, all you have now is a one-dimensional character defined entirely by some combat stunt he can pull off until it, too, becomes old-hat. Not to mention, the next guy can pick the same feats (and skills) and generate the EXACT SAME CHARACTER. Couldn't we save a bunch of time and effort by simply writing “+2 with spiked chains” or something and move on.
This goes double for skill systems. There are finite skills in D&D. Nine times out of ten, you're only going to find a handful of them useful. So, what you're going to do is maximize as many useful skills as your class allows. The other option is to be really crappy at a whole bunch of skills. Neither approach allows for very fast character creation. You see, the designers are hiding the choices behind a smokescreen of apparent choice. If you ignore the mathematically insignificant +1 here and there to some random skills, what you're giving the player actually amounts to “pick X skills to be good at.”
(More or less what you see in Pathfinder and 4E).
Great on paper, but if every character ends up maximizing the same basic skills plus a few class specific ones, then every character might as well just have a +X bonus to a set list of abilities. Even the rogue, the guy with a million skill points, ends up being REALLY good at a handful thiefy abilities and either gains some surprising cross-class skill (“I know a lot about plants!”) or ends up a jack-of-all-trades. It doesn't seem that way when you're creating your character, though, because in order to achieve this effect you're spending 40+ points, adding up synergy bonuses, and factoring in skill-boosting feats and class traits. It's all a lot of smoke and mirrors and meaningless number crunching to arrive at the same place you'd have gotten with a rule that said “you get a +15 bonus with 8 skills.”
Finally, once you introduce one customizable skill, you limit what a character can do. This isn't the same as class abilities, which are things that your character can do because he's a rogue on TOP of things we assume he can do because he's a person. No, skill systems lump all that class stuff together with mundane things like swimming and playing the piano. Now you're asking a player which is more important to him before he risks life and limb in a dark hole filled with traps and monsters: stealth or knowledge: oral poetry? While I applaud the guy who throws a few skill points toward the latter in the name of character development, I'd rather the game rules stopped punishing him for it. Let the rules cover how good you at doing life or death adventure stuff. Everyone's going to max those skills out anyway, so why try to shoe-horn all that together with interesting but meaningless stuff like cooking?
All I really care about for any given skill is the following: do you suck at it, are you ridiculously good at it, or are you everyone else? My character might be a low wisdom slug who wouldn't see a bandit ambush coming if they wore blaze orange and hung up signs (sucks). Your character is an elf with keen eyes and supernatural awareness of the goings-on in the forest (good). Bob's character is a human rogue with no more or less ambush perception than anyone else (average).
Do the rules really need to spend any more time on things than this?