For the record, I do not hate this clan system. I hate not having the old clan system. So here's a possible solution:
Basic definitions
cabal - a group of secret plotters
clan - a group identified by common trait, race, geography, interest, or belief
sect - any group, party, or faction united by a specific doctrine
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Change clans to sects. It would add emphasis to the religious-like fervor that its members are supposed to have.
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With the name "clan" freed up, return the old clan system. It would cross cabal/race/alignment/religious lines and would be nothing more than an RP tool. It would give no skills or benefits.
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Do the magic that would allow characters to be a member of a cabal, a sect, and a clan.
Example:
Evil greedy guy joins the Cartel Sect in hopes of joining the Syndicate Cabal. They kill to make money. But they want to make money selling goods, too. So they start a Trader clan. Neutrals would be able to join. Goods could, too.
The Academy is another good example. Pull in quality people from every Cabal.
Just an idea...
