Imperialus
Explorer
I don't think this is true (or at least it certainly didn't start out as true). As you remember, 3.0e introduced prestige classes in the DMG as optional choices that a DM might want to introduce into his campaign to give extra campaign specific flavour and options.
Now, to my mind it is unfortunate that WotC went hog-wild in producing hundreds of 'prestige classes' which became seen as player focused PC powerup options.
It certainly became a problem with balance when people cherry-picked their way through certain prestige classes (as NewJeffCT said), and the problem existed because of what prestige classes eventually became... but I don't think that they were (or were intended to be) a core concept of the game. The last 3e campaign I played in went from 1st to 20th level without any prestige classes; it was core rules (phb, dmg) + psionics only, no prestige classes allowed. I would say that core concepts of the game couldn't be ommitted - feats, skills, multiclassing etc.
Cheers
Which if you think about it, is also how Kits were introduced in 2nd ed. They were flavor options, that a DM may or may not include. DM's really need to cherrypick what they'll allow.