I know everyone likes different things about a game like BF2, so I'd hate to totally kill the whole commander thing by making him so easily locatable. Combining the first idea in this thread with the most recent one, what if certain spawn points held the artillery, other held the UAV trailer, and others held the Satellite. It would make capturing a certain control point worth something, because then your commander could use the capabilities that point provides. Even though it would still be easy to locate a commander you just make sure that defending the commander is worth something, maybe points.
This way, you don't take away a reason that a large group of people play, you just change the tactics and capabilities a little so they have to adjust. Maybe this would even be just a separate gamemode, allowing servers to run both ways (vanilla commander mode and FS commander mode).
Just some thoughts I wanted to throw in there (and by no means does this mean any of this will happen, this isn't a news release).