The Big Meditation on Factions:
Factions are great. However I never understand why would this character join this particular faction. Why would my vassals suddenly come up in arms to demand external inheritance...while none of them stand to gain anything from it? Why would a small county on the borders of my empire faction for independence, if being independent means it will be Holy War'ed out of existance?
I have no idea how faction-joing works and what is and is not possible, but here are some musings. I wouldn't call them suggestions or ideas. Some of them might actually already be implemented in vanilla/PV and I just don't know about it.
Title Revocation/Free Infidel Revocation
Nobody should join this faction, unless the ruler is a tyrant. So probably only vassals of a tyrannical ruler should join this (if they think poorly of the ruler), and may be paranoid characters.
External inheritance
I have no idea. I can't remember a single IRL civil war with this being the cited cause, but on the other hand I can see why it is there for game mechanics.
King's/Emperor's Peace
There is a big point here. I think only ambitious characters should start such factions. Anybody can join though. I guess.
Independence
De jure vassals should always choose claimant faction over independence (i guess this already works this way). Vassals who border other religious groups or heretics should not join independence factions, unless they are Kings.
Crown Levies
This is the good one I think this one is working as intended.
Claimant and inheritance-law factions work great.
As for civil wars. In case of complete victory for the ruler, I think all participants should be imprisoned. Or the leader should be imprisoned, and the rest prevented from joining factions for some years. Yes.
And I guess it makes sense if faction-joining is disabled for a while IF a faction wins. I am not sure about PB, but I remember in vanilla being caught by Crown Authority faction while barely managing a war. So I gave in to their demands. Guess what? All the same people just reformed the faction and asked crown authority to be lowered AGAIN.