I'm thinking Snake's super would be him calling in a Metal Gear and firing off nuclear missiles randomly all over the stage, that would be so freakin' cool.
As for his taunt, I have several ideas as to what I think it should be:
Snake busts out with a cig and lighter lighting the cig, taking a hit then letting the smoke out then quickly putting the cig and lighter back up. I'd say the animation should take.... 5 seconds?
Snake does a Salute.
*random codec call* then Snake answers according to what the person tells him. There should be some serious ones and funny ones, it would be a cool idea.
Snake points out and says, "Do you have what it takes rookie?"
OK, good enough for now, haha. Um, As for the box... I'm thinking it shouldn't be incorporated within his moveset, I honestly think that would be a dumb idea, if anything, it should be his shield, or just not have a box @ all.