Even an incompetent commander still has access to unbalanced powers. It doesn't take much experience to know "right click and press UAV" to have a free unkillable spotting tool that spots even inside buildings. Or "right click and click quick deploy" to give a squad a half redeploy wait time. When there are 2 commanders competing, it's a bit better, but that's pretty rare these days, so it usually devolves into one team having a pretty significant advantage.
I've shot down the UAV's with the AA several times. This of course requires people to use the AA as an AA...which will piss off the run-n-gun pukes but that's what the AA is supposed to do is to suppress the enemy air.
Also, I'm not opposed to the unbalanced nature of having a commander on one side and none on the other. Happens all the time in reality.