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So. I don't feel like reading through all the posts. Is this still a thing?
One idea I'm going to throw out is that guilds are maintained as an NPC only organization. The guild tutors become the GMs, the halls are made open to the public and picking the class of an associated guild gives you access to a channel for that class shared among the org (this is to help with skill specific questions and the like not as a guild replacement). The guilds would not have any ranks/political power or be a thing as far as players are concerned. It's just an NPC-only org and everybody of that class in a given org shares channel automatically.
This frees factions to be political/ideological entities separate from guilds, although they can claim influence or inspiration from the guilds. It also means that for instance the guards are still members of whatever guild they're hired from, they are just hired by any of the factions.
I'm totally shipping @Eliron and @Everiine now.
You gotta risk it for the biscuit.