It seems to me, it entirely depends on the games you run as to what kind of prestige classes work.
Mike implied that, in fact, there were two kind of prestige classes, and I'll name them here: There are Organizational Prestige Classes (OPC), where you are taught interesting skill sets, spell, etc. from your membership in a certain group, and there are Specialization Prestige Classes (SPC), where your character gains different skills based on focus in a certain discpline.
|When intrigue is the name of the game."Chess" by Moyan Brenn|
Where OPCs are useful though, are in campaigns where the PCs are involved with intrigues or politcally motivated adventures. Plots such as "The PCs are hired by the local king as a 'strike team' to cripple a rouge nobles rise to power" could easily see a need to become specialized, and very interesting political potentials come in with OPCs. Say a Order of the Wyvern wizard is hired into this strike team: the Order could say the local king owe them a favor, like that graveyard full of old warriors, which makes the king wary of this Wyvern Wizard. If you run those kind of adventures, OPCs provide a ton of new NPCs to add to the mix.
That being, said, if you do have a intrigue based plot, these SPCs will work great too. However, that PC won't be part of a "pretisgeous" club, and therefore wont have those contacts and other NPCs to lean on. Not bad at all, especially if your plot is more like "The PCs are a band of sherrifs coming to clean up this evil town..." kind of story.
As a note, OPCs work great for NPCs, especially antagonists, becuase it adds flavor, complexity, and contacts to the bad guys. Nothing like making a Arcane Order mage a bad guy, and watching as the PC's bust down the doors on their next budget meeting.
Thus and therefore, I think there should be more of these specialist type prestige classes than organization-based ones, since the specialization can be used anywhere. But, OPCS are useful for intrigues, politics, and antagonists, in my opinion.
When it comes to Duet gaming, I think either prestige class type is great, but one can really explore the intrigues and politics of an organization based class with a one-on-one type game. Not to mention, but the organization itself becomes a source of adventures, as the higher ups in the org could suggest/command your pc to go on missions, and the PC's membership alone could cause other factions to become the PC's enemy...
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