My biggest gripe with prestige classes is that there are too many 10-level classes as opposed to 5-level ones.
As I see it, a prestige class ought to fill one of 4 major functions:
1) Special training unique to a particular organization, or class of organizations, like the Vigilant from R&R, or the Assassin, or the Tatooed Monk from OA, to name a few.
2) A fighting style. This would include many of the clan-specific PrC from OA and Rokugan, and could also encompass things like the Weapon Master and the Iaijutsu Master.
3) Either a new type of magic, or a very specific focus on one area of magic. Good examples of this would be the PrC's from Occult Lore and Spells and Magic.
4) An extremely specific supernatural ability, like the above-mentioned Bear Warrior, or the Dragon Disciple.
As I see it, in most cases, categories 1 and 2 would be better served with 5-level PrC's. In a world with normal D&D demographics, 10th level is fairly high, so it would seem sensible that most organization training and fighting styles could be "mastered" by 10th level, with 5 levels in a core class and 5 in the PrC. Sure, a few classes like the Iaijutsu Maste that represent more a philosophy of fighting than a specific set of maneuvers could be 10-level, but they should be more rare compared to 5-level classes.
Category 4 would also be served better with 5-level classes. If all you're doing is developling some supernatural ability, like polymorphing into a bear, or slowly turning into a 1/2 dragon, why stretch it out over 10 levels, half the career of a non-epic character? A 5-level progression would work better.
As I see it, only new types of magic more or less require 10-level classes, since they fundamentally change the way a caster works.
drquestion
P.S. - So that I don't completely ignore the original question of this thread, my least favorite PrC has to be the Shadow Adept. He essentially loses nothing, and gains a bunch of supernatural abilities.