Even thunderbolt is pretty rare, tbh. Most misdreavus really enjoy having a substitute cause it lets them get past the number one way to kill her - Sucker punch. The priority move has a whopping 160 base after SE multipliers, and thats before STAB, hitting on her weaker physical defense side. Thusly Sucker-punch is really the best way (offensively) to deal with missy. Some good non-stunky Sucker Punchers are Houndour, Murkrow (who also retains neutrality and resistance to the two most common offensive moves (shadowball / HPfighting), and Pawniard. Pawniard and Houndour are both weak to fighting and ground though, so they maybe hard to just slap on a team. A missy of your own can deal with missy, if you're lucky on the speed tie - though thats a horrid answer. Aside from priority, Outspeeding missy is good. Strong scrafers such as Murkrow, Misdreavus, and even Porygon, can outspeed and either Outdamage or OHKO Missy depending on circumstances. Missy is such a threatening and versitile mon because it is so hard to deal with when it sets up. If you're dealing with a +2/ Sub'd Missy, you're in trouble. Keeping offensive pressure on missy when she shows up (though easier said than done) is another good way to deal with it - A move doesnt have to do SE damage to take out a Substitute.