Recommend giving each additional player in the campaign their own commander. Letting each player customize their own commander that joins the co-op will greatly increase the replay value of the co-op campaign and provide more things to do to additional players. If challenge and difficulty is an issue I recommend adding a separate co-op campaign tracking similar to halo how co-op wins only count for co-op and not single player if people want to beat the campaign by themselves and let everyone know how hard they had it.
