It occured to me that another way to deal with auto resolve could be to allow each commander to choose 1 battle to command personally, BUT if they both pick different battles then both battles will be fought RTS style. That way you still have to prioritize which battles are most important for you to win.

My main concern is that currently a player who is good at the RTS part of the game has a significant advantage in a multiplayer campaign. He can easily win by personally commanding each battle. Limiting the number of RTS battles will help make the strategic map a more significant part of a multiplayer campaign.