I would love to see what they could do with the clone wars. I think the greater numbers of jedi would create some intresting match ups in how to balance out jedi vs droids. I respect what has already been done this would be a new challenge for Petroglyph, something I would like to see them work out. I think if done right the force can be exciting while still remaining reasonable as to not effect normal tactics to much.
I also think if they did create the clone wars factions as new factions they would also try to give the OT only fans some things as well. There is no reason why they could not add a few new ships/troops.vehicles and options to the old OT factions as well.