It seems like it would be good to have a support commander for the important star systems. I mean if we are talking about an entire galaxy to cover you should have a step up from normal engineer units. Plus it could possibly make a good end game unit. I believe that Supcom FA did a pretty good job with support commanders. They were more high stakes engineers, but cost a good amount of money.
Neutrino has hinted at being able to "replicate" your starting Commander during the late-game... At great cost of course. In my personal opinion Support Commanders were broken in SupCom. They generated too much Mass when upgraded. I hope, in Planetary Annihilation, the Commander is unique in his ability to do so as a mobile unit.
I liked the decoy commanders in Total Annihilation. They couldn't really do much, but you could have them walking around in your base making a late game commander snipe really difficult.
