Personally, I think that prestige classes shouldn't be bound by the idea of 5 or 10 levels. True there are quite a few 3 level prestige classes and a handful using other numbers, but my point is that prestige classes shouldn't necessarily be so uniform in the number of levels. My favorite prestige classes are those that tend to be thematically inspired and don't have filler levels ("empty" levels simply there to push the class to level 10, for instance).
I think prestige classes should be designed not to a specific level, but simply to the level necessary to both capture the feeling of what's being presented and offer the abilities that make it come to life. If that means 3, 5, or 10 levels so be it, but there should be just as many prestige classes that fall somewhere in between.
Of course, I'm a storyteller, not a number cruncher. I'm sure there are systemic reasons for the uniform approach to prestige class levels, I just don't see the necessity.