Is there anything in particular that the team was built around? I ask this because based on what you're building around, the team could have different end results when I make changes to it since I try to keep the theme and main goal of the team when I make changes. If I end up making a full rate for this team, I'll address the problems in greater detail, but since you wanted to know what could beat the team, I'll mention some threats here.
The biggest threats I can see are fairy types in general. Breloom and Mega Latios are forced out by them and you have nothing to reliably switch into a fairy type move. Your only answer to them is Bisharp, which can't switch into fairy types because it gets 2HKOed by their STAB moves. Clefable is the only exception to this, but only because you put max HP EVs into Bisharp (which should definitely be put into Speed if it's kept). Regardless, it doesn't want to switch into Thunder Wave or the somewhat uncommon Flamethrower.
Mega Scizor is also a huge problem to the team, mainly because there aren't any SpA EVs on Thundurus and because it lacks Thunder Wave to cripple it (even with the proper Thundurus set, Mega Scizor is still very threatening). Because of the lack of power from Thundurus, your whole team is walled by Mega Scizor, so it's free to set up on everything but Manaphy. Your best answer is bringing Manaphy in on Scizor before it sets up, and if it does set up, hoping for a Scald burn.
Since I don't want to go too in-depth into each threat, I'll just list the next few threats with a small description on why it's annoying. I can elaborate more if you want me to, though. Other threats are Kyurem-Black (nothing switches into Ice Beam that can force it out; Breloom and Mega Latios beat it 1v1, but can't reliably switch in), Mega Heracross (sets up Substitute on Breloom, Bisharp, and Donphan; can KO everything else once under a Substitute with its coverage moves; Mega Latios beats it 1v1 if no sub is up, but can't reliably switch in), and Serperior (fires off a Leaf Storm on Donphan and Manaphy, beats almost everything else at +2).
