I like the idea of including holy orders as independent factions -- perhaps as mini-factions with extremely limited territories, but highly advanced units.

The difficulty IMO would be programing them to interact with the player and other factions in a somewhat historically accurate manner, and befitting their somewhat unique goals and objectives (i.e. not necessarily seeking to build a kingdom).

Otherwise, they would be just another Catholic faction with a special name --something I would find somewhat disappointing.

Guillaume