If the tornado was as simply as dodge and punish you wouldnt see most guides, posts even in this forum suggest you spam it for damage.
I play MDK's meta and I can assure you in the right hands The tornado is pretty much unpunishable after its done if your using it correctly, once you space yourself after the lag is minimal enough that you can avoid being punished., unless the Meta makes a spacing mistake or the opponent has a fast projectile.
Anyway moving on, with snake, the grenades are the counter to tornado, if he wants to spam tornado try to keep a grenade in hand so that when you go to roll away or block it, the tornado sets off the grenade.
Depends on your character, some character simply wont be able touch him.