In my opinion the Commander is basically a very good idea. The problem is that it got ruined by some jerks fooling around and players not following orders of a able commander because they think they know better or just want to get kills and ignore the overall situation.
All those things can also happen in other areas, like a noob taking the KT, or squad leaders not going for the important positions, or squad members wandering around instead of sticking to their squad leader.
Fact is that the commander can dedicate all his time to follow the kills and whats happening on the map and so get a good knowledge on whats going on and direct the squads so that they are distributed for maximum efficiency. A squad leader can only afford a quick glimpse every now and then at best. And the random distribution of squads you get without a commander often fails and leads to losing the map.
So in my opinion, having a good commander can make the difference between winning and loosing a map.
The commander artillery also needs some skill to use properly. You gotta make the decision on what flag to use it, based on where your team currently is and also decide on the timing. You might make some kills anyway, but without some planning it fails to help your team advance and then you gotta wait quite some time for the next try.
Of course on some maps like PDH, with just one flag to attack, the commander artillery might seem too overpowered and cheap, since there is not much tactics involved there.