most of the PrCs seem to come in one of three flavors:
-Membership in some organization: Fist of Hextor, Mage of the Arcane Order, Knight of the Middle Circle, or..
-Specilization in one aspect something you can already do: Order of the Bow Initiate, Mindbender, Tempest, or..
-Hybridizing some of Class X abilities with Class Y abilies more smoothly then you would get by just taking 50/50 in each class: True Necromancer, Arcane Trickster, Warpriest.
I think PrCs that focus on one aspect should be more powerful -in that aspect- then a single classed whatever who can do that one thing pretty well, but still all the other things associated with their class just as well. Should a Fighter 10/Deepwoods Sniper 10 be a better archer then a Fighter 20? Yeah, I think they should. That fighter 20 will have so many feats left over as to be able to diversify their abilities.
PrCs are also kinda limiting in and of themselves. If you're a 7th level rogue and you make enough exp to reach 8th level, you can't just go.. Oop, okay. I'm a Shadowdancer now. Go me. Nuh uh. Find someone to train you. Gain entry into that organization, find the esoteric master and convince him to teach you his Hidden Arts, come into contact with the Forbidden Powers and learn the Terrible Secret of Space. Once you've gained access to a PrC you should have earned it, at least in some way... and more so then just taking X feats and some ranks in Y skills.
That way I have no problem in having PrCs being more powerful then a single classed character.