I dont know how this would be implemeted but here is the idea:
Make ALL armies "Crusades"/"Juhads"...so you dont "make" troops in an unrealistic "RTS" like fashion...
Like if a Roman general wants to launch an attack on a settlement or wants to reqruit an army he asks the Senate (insert Pope but invisible somewhere on the corner of the map) for armies...this way you may have a realistic legion that has desertion...
For other factions it would work in a similar way...
This way you may provide an overhaul to teh idea of the campaign and make it faaar more realistic than the RTS like upproach...