My problem with 3.5's prestige-multiclass system is that it went too far in enabling players to customize their characters beyond what the genre should support.
In an earlier iteration of D&D (say Basic D&D, or AD&D 2nd edition), the class system could be frustrating because it made it impossible to create a character like Conan (who had thief-like stealth and climbing combined with a fighter's strength and prowess) or Rand Al'Thor (who was a master swordsman as well as mage). Given that these sort of hybrids are common archetypes that we all enjoy reading about it, it's no surprise that players would want the ability to make heroic, well-rounded characters of similar ilk.
But in enabling unlimited multiclassing, with "dips" in to a class to scoop particular powers, and endless variations of prestige classes, characters went from too bland ('a fighter') to too spicy ('a half-ogre fighter/barbarian/ranger/templar/dervish') and missed the sweet spot. The characters that are created don't feel like the fantasy heroes of myth, legend, and fiction. They feel, at best, like the wierd quirky side character that shows up in one chapter and interacts with the real hero.
The root cause of the problem is the irregular distribution of benefits from leveling. Simply put, some levels of some classes are not worth as much as some levels of other classes. As a result the min-maxing player will switch out of classes when they are no longer optimally beneficial and find a new class that provides better benefits for his intended purpose. The net result is that a character who skims through a bunch of different classes is far mor effective than one who levels up consistently as a fighter or thief.
This is, of course, the opposite of the real world, where specialists trump generalists in most fields of endeavor. Gold medalists in track don't switch to swimming in between the summer games. Chess grandmasters don't play Starcraft to tighten up their openings.
With neither narrative feel nor realism to support the hybrid class character generation, the system is inherently going to lend itself to min-maxing.
You sure aren't playing a Svirfneblin Red Dragon Disciple because of a character concept.
