I don't know how Sammael can say the current (pre-4th edition) stat system is meaningless and arbitrary. Check out any of the JRPGs. Those have meaningless and arbitrary stat systems. When a character's stats are 100x higher than they previously were, they're doing 1000x the damage, and the character is supposedly only slightly stronger than he was before, then it's arbitrary.
The D&D stat system appears incredibly meaningful. And I'm not saying that simply by comparison.
I love Prestige Classes. I just think they're abused. Maybe they were introduced poorly. Maybe enough emphasis was not put out that these are not meant for everyone. But, it's probably largely the schism between people who want to roleplay and those who are just gathering to kill imaginary things. One doesn't see how he can join some order of wizards he's never met before, the other just sees that he gets a nice new ability that lets him kill even more goblins.