First and foremost, several (read most) PrCs are… disappointing. You have already expressed… um… displeasure at quite a few of the PrC choices out there. I/we need to decide which ones are worth being PrCs, which might be accomplished through a different mechanic (such as base class options or extra feats), and which are 100% pure crap.
Secondly, my take on Prestige Classes are that most of them are "secret societies"… you don't go to them, they invite you. Some of the baggage that goes with that is that I have to develop places and people to match the PrCs. For example, Dwarven Defender should only be available from a Dwarven city - like an Ironforge size city. There's probably three cities of that size in Europa, but you (and I) haven't found them yet (although some people are warm… warmer… hot…). Similarly, Arcane Archer would have to be granted by high-ranking Elves… when we find them.
For something like Archmage or whatever, there has to be "Towers Of High Wizardry" for prospective members to study at. Although there might be a number of wizardly schools throughout the lands, a "Tower Of High Wizardry" must be something fairly rare… maybe one in Brython (or one in Celt lands and one in Saxon lands), one or two in Italia, one or two in Greece, and one in Egypt? Maybe one only in Europa for each School of Magic? Interestingly, I pulled up the list of medieval Universities earlier this week, with a bit of that world-fleshing-out firmly in mind.
Third, there should be lots of roleplaying overhead that goes along with a PrC. Gaining the first level in a PrC should take a month of game time, at the appropriate training facility… not half an afternoon with some grizzled expert. Indeed, for many PrCs, there should be tasks/quests to make oneself eligible to join. After you have joined, there should be Codes of Conduct, compulsory meetings, reporting to superiors, membership fees, members "business" (more tasks/quests), and more.
To get in the mood, think about the Knights Templar, the Freemasons, the Pythagoreans and Neopythagoreans, the Rosicrucians, the Thule Society, the Thugee cult, initiates of the Eleusinian Mysteries, the Roman Catholic Church and many more real world examples. The key features of all of these organisations are that: (1) they are exclusive; (2) they claim to own special secrets; (3) they show a strong inclination to favor their own [[http://en.wikipedia.org/wiki/Secret_society]]. And after all, isn't that what a Prestige Class is? Exclusive membership, special secret knowledge, collegiate favouratism?
In short:
- PrCs need to be carefully vetted for "worthiness";
- World background material needs to be developed;
- PrC organisation material needs to be developed;
- Players need to be prepared to invest in a PrC;
- Invitations need to be sent out :D
PrCs are meant to be exclusive and special - I wanted to make sure they were so.