There's not many true RTS games out there, I think ZK should stop turning into an RPG and instead start to keep up the desire for a true RTS.
I repeat myself: Commanders should be commanders. No experimental weapon platforms; no porc-busters; none of the current existant unit roles.
It should be a unique unit with the ability to turn the tide of battle with other means than sheer hp, firepower, speed or range. There already are
several high hp, high firtepower, long range units, units with shields, units that jam, units all kinds of weapons and so on. I really don't see a reason to add another such unit only for the sake of being a players avatar.
Instead let a commander be the very unit that represents the game and the player. Zero-K's scale and awesomeness and the player's style and choices.
Nerfing Skuttles, which - like nearly all cloaked units - can be guarded against very easy, will result in turning the unit useless. Simple as that.
The argument that 5'000 metal units should not be countered by 550 metal units which require insane micro, while they in return can be countered by 100 metal in units with less than half the required micro is REDUNDANT!