Red-eyed dust bunny
Ah. Even the core book made a few recommendations along those lines. But I tend to think balancing mechanical benefits with social drawbacks is futile. Prestige classes also lack focus, are inherently biased toward certain classes/builds, and aren't integrated well into the setting. Some are almost purely mechanical (for instance, the multi-class enablers like mystic theurge), while others implied a sect or cult or other tightly-knit organization. But without a setting, they just kind of floated. Cryptic Alliances were well integrated into the setting, represented something very specific and uniform (didn't try to mix in archetypes, for instance), and didn't provide mechanical benefits.3.X version, page 210. Test-based prerequisites for prestige classes.
But that's probably drifting off-topic a bit.