Personally I don't think the commander function itself is the problem. People are the problem. Passing the blame, lack of experience, refusal to co-operate, and so on... all human factors. There isn't much that you could change in the commander function to mitigate any of this.
I'm in New Zealand. So when its evening here, its midnight in the US and early morning in the UK. Servers are quiet. I try not to use commander too much since there is a bit of a stigma around using it in small games. However I will sometimes take the role if it becomes too much of a stalemate. It has been a decent opportunity for me to learn and become more fluid with the hotkeys. Also credit to Blackhand for his youtube videos.
I joined a match the other day on Islands where the bases had been reduced to just the Barracks and Hand of Nod. The match had been going for over an hour. Nobody wanted to vote for a commander I assume because player count was low. So after about half an hour longer of failed infantry and APC rushes I managed to convince people to vote to change the map.
This is also a problem with people. The commander function wasn't even used so you can't blame that. Without doing the map change vote it likely would have gone on for hours, like it some times did in C&C Renegade. But even with what happened I feel cheated of a natural ending, win or lose, that could have been achieved by working as a team and electing one person per side to co-ordinate.
IMO it's the stigma around commander that needs to be scrapped. If we can do that, and allow people to learn how to use it more effectively, then maybe we will solve more than one problem.