Perhaps just have region-specific units - such that whomsoever owns the territory gets to recruit whatever, much like in some of the mods for RTW... With a smattering of faction units that can be built anywhere, would provide for enough variety between factions, and allow for variety within a faction dependent on the territories being fought in. Perhaps a slight boost for units native to a faction, or an increase in cost for the local levies...

As for vassals sending troops to fight - sounds good to me. Or perhaps getting them to send armies against a target of your choice (hijacking the crusading code for this might be an idea...)