Here's the best counters for the thing. Of course, the charge moves backed by Mewtwo's power change a lot of these would-be counters and the increased +6250 HP this has doesn't help matters (18,750 HP as opposed to 12,500).
That said, the overall best go-tos are Mewtwo and Tyranitar. Mewtwo isn't weak to a single moveset and lasts a while, while Tyranitar only fears Focus Blast and packs a decent punch.
Additionally, weather is going to be your best friend. Stuff like Rain can boost the Bug-types and make Raikou / Zapdos / Kyogre pack a punch, Windy helps Rayquaza, Dragonite, and Salamence do some excellent damage, Clear boosts stuff like Moltres and Blast Burn Charizard, and Foggy (if you can afford it) boosts the aforementioned Tyranitar and Gengar as well as Houndoom and Banette. Other less lucrative options include Dragon Tail / Sky Attack Lugia and Bite / Crunch Gyarados.