How are you supposed to fight a commander that's underwater in the early game? Surface ships won't attack them, sub's won't attack them, and torpedo launchers won't attack them. Short of nukes, it seems that bombers are about the only thing. Playing a game earlier today on a large island map, I had another player spawn close to me in the ocean. They used their commander to kill my naval units and defenses, and uber'ed my naval factories. With nothing to stop them, his ships moved in, while he danced his commander in and out of the water one-shot killing my shore defenses. If the commander couldn't use his weapons underwater, it wouldn't be as bad, but as it currently stands, there isn't much way to deter an underwater commander without masses of aircraft.
That is too bad, at the moment it can sort of be considered an exploit as the subs are not fully integrated. At that point I would have focused on bombers and cruise missiles to take out any navy he was blocking your recovery from. Do you think cruise missiles would have been able to target the commander as well? I have not tried. In any case, when I realise that I am doing something a player cannot counter because it is feature complete (such as hovering a commander around in the lander) I stop what I am doing and put the offending unit back "in play". It's silly to win with tactics that will be eventually irrelevent. in other words, you played against a jackass
Once we have fully functioning torpedoes and units to use them it should be fine....that said using energy weapons underwater seems a little strange to me...