My point wasn't that all manaphy can beat all kyogre(sorry for any confusion), but that Grass knot manaphy OHKOes bulky kyogre after one turn of setup and that CM manaphy sets up on scarfogre, ruling out kyogre as a hard counter.
@tehy: I understand what jackm was trying to say and I addressed that in my previous post... and grass knot is sorta rare but is isn't unheard of.
Also, spamming rest as kyogre thunders is indeed a bad idea, but in theory manaphy can CM as specsogre switches in, then comfortably stay in the following turn and scald fishing for burn hax while surviving one thunder. If kyogre gets burned, great, if not, oh well, and manaphy can switch out the following turn. Then it can rest up later against something like support dialga, forretress, or one of the blobs.