3e was designed with the idea that disadvantages can be abused and are fairly unbalanced.
So, instead, everything has a "cost." You need to get a certain score to get a certain thing.
The problem with disadvantages is that they're not universal, and they're stackable. A wizard probably wouldn't mind having a feat that gave them a minus to weapon attacks and damage in exchange for a free metamagic feat -- they're not going to hit often or do a lot of damage anyway. So their gain is greater than their sacrifice, for that character. If he can do that over and over again, it becomes quite unbalanced.
Again, something like Blindness may be a severe disadvangate for a normal character. But then you, say, take a character that has blindsight and give him blindness, and whoop-dee-doo...you've compensated for it. Or take a psionicist and make him blind, and he suffers less, but gets the same reward.
It depends on the campaign, too. Being Hideous in a campaign based on a dungeon-crawl isn't going to matter too much...most people will take it, because it provides an advantage for very little disadvantage. being Hideous in a game based on intrigue and politics is going to cripple your character -- people will take things that will give them physical penalties for social bonues, instead.
It doesn't work too well, thusly. 3e was designed to be a cost system. Meet the minimum points, and you can choose one option, or another one, both of which are about equally as powerful (in theory). Start inserting diadvantages, and you'll have a complex stew of blech.
