If not all minor factions should be enabled in a game however, or at least in the future when there are many more minor factions, perhaps it would be cool to simply have a drop down to have randomly add 'none/few/average/many/all' minor factions.
I like this idea too, especially as the number of minor factions increases. As it is now, I always play with all of them enabled, but if the number were to say, double, then the game might become more about minor faction management rather than trying to defeat the AI.