Anyway, onto counters:
Top 1: Ferrothorn. I HATE THIS THING WITH A PASSION!. Even Kyogre is scared of this thing.
Top 2: Almost every Arceus forme. Specifically the Normal variant
Top 3, Palkia. If manaphy has no boost with Tail Glow / Calm Mind
To offer some value with this post, I behoove you all to observe a powerful and little-known set posted by Jackson12 of Smogon Forums, I feel like this set has the ability to dominate Ubers in the right hands and its being posted on the site can spiral Serebii.net into legitimacy.