New York is a very special state to me.
Anyways, so me and kinzer did a bunch of testing this weekend. And lol, in 20 minutes of testing, I couldnt get the fsmash to hit MK through the Nado, although somehow I managed it later in a real match against an MK(which I won btw ahem. Die MK). Bair is hard to space appropriate, but its doable, as Puffball definately shows in his vid.
But your best options? Almost always spring and homing attack. if you are directly above Mk, just spring. I would actually recommend baiting MK a bit if you are above him; make it look like you are going to fall down into the nado, and then just spring up soon just slightly ooutside of the nado's range. It wll almost guarantee a hit, and at worst, if he moves, you'll escape freely.
Homing attack though is seriously too good. If you know your homing attack angles well, you'll be hitting MKs out of nado too easily. basically, if you are anywhere to the side of the nado and parallel with/above the top line of the nado, then you ll hit Mk ouot of it. The arching motion of HA makes its so that Sonic travels right over the nado's hitbox into the center.
Seriously, there was a time when Kinzer was just moving all over the stage with nado trying to catch me, and I went to pick up the phone and did nothing but press the B button alone repeatedly and hit him out of nado like 90% of the time.
The biggest problem was when MK did a rising tornado, but I have a remedy for this XD.
Ok, so homing attack is such a slow move, that we almost always cancel it for the shorter charge length. Just from watching videos, I can tell that rarely does anyone go for the non cancelled version. Well against a rising tornado, the best thing to do is not cancel the homing attack if you are not above the Nado. Dont cancel HA, because that way the HA rising with the nado, making help you hit rising nados.
So yea, HA=Nado Counter. Ok well maybe not counter, but if generally your best option, you are much more likely to connect by jumping> HA than risking an fsmash or Bair unless you have amazing spacing ability with that bair. If you are directly above nado, then spring to safety, simple as that. Don't be afraid to using homing attack. Its such a noob tactic for some, and I see few Sonics actually use it. Against the nado, it really is awesome. Go and test it yourself XD, if you know the homing attack's angles well, there should be no reason why you aren't connecting with homing attack enough to make it unviable for the MK to spam it.
If you get caught in a couple of nados per stock no big deal. Its no different from being punished by a couple of aerials instead. There not exactly much you can do if you are punished with a Nado, same as there isnt much you can do if you leave yourself open and are punished with a dsmash. If you predict the nado, or just want to control spam, then HA and spring are your best options.
Also, I saw homing attack go through MKs Fair a couple of times O_o. I think I might have just gone through it in between hits, or riiiighhttt after his fair finished, but it happened pretty often. I actually think HA is a great punisher in every matchup, so use it =P.