The first Pokemon I thought of naturally to combat the MoltTops core is Galvantula.
Timid @ Life Orb
252 SpAtk/252 Spd
-Volt Switch
-Thunder
-Energy Ball
-Hidden Power Ice
Galvantula alone is able to come in after one of your Pokemon has died (or against a predicted Roost or HP Grass from Moltres) and OHKO both of these Pokemon with a Life Orb boosted, STAB, ~93% accurate Thunder. Both Moltres and Tops are OHKOed 100% of the time.
**EDIT: I realize I was supposed to come up with a "Counter" to this core, but I have to go to school right now so maybe when I get back haha. Galvantula does dismantle it though.