Hi KidMagic, so although you have two boosting 'Mons, I presume this team is more about luring the right 'Mons w/ Thund, Azu, n' Serp to set up a nice clean with either Hoopa vs. Offense or Medicham vs. balance w/ Heatran as support, so the changes I make will be based on this assumption and your team building process.
I think you should go with Prankster > Defiant and Thunder Wave > Knock Off on Thundurus. Your team has numerous ways of dealing with Lati@s as it is (especially with TauntTrapTran), and honestly I don't think Defiant is doing much for you here with Fighting/Dark as your physical coverage. Thunder Wave allows you to check set-up sweepers that really give your team trouble, like Charizard-X, Altaria (Jolly Altaria, a pretty prevalent set, can get a boost on Serperior, Hoopa, or Thundurus, OHKO Azumarill after Rocks and outspeed Hoopa, and sweep the rest of your team), Mega Gyarados, Mega Ttar, etc. Also, TWave allows you to threaten Alakazam and Aerodactyl, two Pokemon that outspeed Hoopa and can run through your team if Azumarill is chipped.
To remedy the offensive pressure lost with Knock Off, I would use Toxic > Flash Cannon on Heatran. Flash Cannon with almost no SpAtk investment isn't making much of a difference against Fairies here. I assume you're currently using it to hit Clefable, which is beaten by Taunt + Magma Storm already, and doesn't have much room to set up given all the offensive pressure you already pack on this team. Faster/boosting Fairies such as Altaria and Diancie typically pack coverage to beat Heatran regardless, and Taunt + Toxic beats all the bulky Refresh/CG Altaria sets anyway. Toxic allows Heatran to check other boosting threats such as Charizard-X and Volcarona, putting timers on them. It helps a ton though with bulky Pokemon such as Hippo, Slowbro, Cress, SpDef Talonflame, Mew, and Tyranitar, which really helps your heavy hitters (Hoopa, Thundurus, Medicham) break through opposing bulky balance teams. Also, I'd just run max speed on Heatran; the difference in damage output is negligible and sometimes getting the faster Taunt on opposing Heatran (preventing Rocks n' stuff!) could be worth it in certain situations.
As a nitpick, I'd heavily consider going max speed on Hoopa, since getting the jump on ScarfTran is awesome, as well as being able to at worst speed tie with +1 Altaria, which can grab a boost on a number of Pokemon and sweep your team (it OHKOs Azumarill after Rocks). This isn't really as relevant though if you implement the next change I'm suggesting, but it's a real change of pace from the original build so I understand if that's like, not something you're into.
Finally, I'd suggest a change of Slowbro > Azumarill. While this makes your team weaker to Weavile (although given Poison Jab Azu can be a shaky Weavile check as it is), Slowbro really helps out your team in terms of giving you a Scald absorber (a really solid Keldeo switch-in, which you currently lack), a physical weather check (meaning Excadrill, Kabutops and Swampert don't run through your team), and a Fighting switch-in (to opposing 'Mons like Medicham and Lopunny, which you basically rely on Hoopa just to RK). It gives you an easier time against some other physical threats like opposing Azumarill, Altaria, and Jolly Talonflame, especially since Heatran can be chipped easily, and generally helps your Pokemon by spreading residual damage through burns. You can run Fire Blast > Psyshock since Keldeo still doesn't break you any time soon, and this gives you a much more direct way of luring Ferrothorn, rather than having to find a chance to BD and then Knock Off with Azumarill. Fire Blast also allows you to handle Weavile to an extent, sponging a Knock Off and then KOing it after Rocks + LO damage. Although since you can smack Weavile w/ TWave, I'd also suggest keeping Psyshock and throwing on HP Fire > HP Rock on Serperior, since Thund is gonna be your main weapon vs. ZardY and Slowbro + Heatran can handle Flying-types well enough so that Serperior can sweep with a bit more ease (and also prevent Bisharp from setting up, which is big!). Just having the better coverage overall is awesome pretty nice imo.
^ With this change you can keep Knock Off on Thundurus, although you'll still lose out to some stuff like Alakazam if you don't keep Hoopa healthy
Anyway, there are some things I didn't really address, like a Bisharp weakness, but I think these changes will make your team more consistent and ultimately better support your heavy hitters to comfortably clean late game.
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