I plan to give companions some use in the war minigame, but I'm not fully decided on the specifics yet.
The plan I have right now is to make a "leader squad" unit type, which will contain your main character and the companions you selected. Companions will affect not only the strength of this squad, but will also give you special abilities. Slots for the leader squad will be limited at the start so you will have to chose who to pick instead of taking everyone.