I think the problem of PrC is in their requirements.
Ideally, they should be very simple. One or two mechanic conditions (among X feat, Y rank in a skill, or ability to cast Z spell); and an in-game condition (joining a prestigious organisation).
But what we've got in half a dozen or more mechanic conditions (requiring at least one feat, at least 3 skills, a minimal base attack bonus, etc.). And the in-game condition is most usually ditched altogether.
That's what make PrC so unwieldly when designing NPCs, if you want to do them by the rules.
It would have been better for PrCs to have simplest prerequisites, but be always associated with an organisation, secret or not. Then, multiclassing in the PrC would require merely to find and contact said organisation, gain their trust, pass an entry test, and if successful, congratulations, you're in.
The prerequisites would be dissimulated in the test.
For examples...
Rather than a minimal BAB score, the character could be tasked off slaying a family of ogres single-handedly. A guide lead him near the den where the monsters have been seen, and there he goes.
Rather than merely the capacity to cast spells of X level, the character's spellcasting could be tested against specially made spell-resistant items.
Rather than X ranks in Move Silently, Hide, and Open Lock, a character could be tasked to retrieve a particular item somewhere in a noble's mansion.
And so on.
Prestige classes whose joining would be fully roleplayed, ditching most, if not all, of the mechanics. People would be less likely to get into multiple prestige classes combos, because their loyalty would be questionned, and it would put the prestige back into prestige class.
