Mewtwo is pretty much as powerful as a low-level Dragonball Z character and could probably destroy the world with some effort if it really wanted to. So of course a metal sea-serpent shouldn't be much of a problem.
Speaking of overpowered psychic types, Metal Seadramon protects his body well, but has an unprotected mind. He's very vulnerable to moves like Hypnosis, Dream Eater, Dark Pulse, and maybe even stuff like Confuse Ray or Swagger. With this in mind, Darkrai, Hypno, Gengar, and Crobat all stand a chance.
Next you can factor in the fact that Metal Sedramon is obviously a Steel type, probably Dragon-Steel. He doesn't Levitate, which leaves him vulnerable to the moves Earthquake and Earth Power. The best Earthquake/Earth Power users are Groudon, Arceus (especially with Earth Plate), Landorus, Diggersby (HUGE POWER!), Zygarde, Garchomp, Mamoswine, Excadrill, and White Kyurem since White Kyurem might not get STAB but has god-like SpA to pull it off.
Steel is also weak to fighting. Metal Seadramon would have to watch out for pretty much any Fighting-Type Mega Evolution, all of which could crunch up his digizoid armor like an aluminum can, Conkeldurr, Machamp, Breloom, and Lucario. If Meloetta could get into Piroutte Form, she could kick that dumb sea serpent's butt too.
Lastly, we have Legendary pokemon that have abilities that predispose them to Victory. This includes Victini, which always wins in the end somehow, Mega-Rayquaza, who is overpowered and versatile enough to take anything Metal Seadramon can throw at it, Yveltal, who could turn it to stone without much trouble, Azelf, who could drain away its will to fight, and Giratina, who could phase through Metal Seadramon's Armor and bite at its soft weak flesh.
There's probably more I'm not thinking of, but that's all I got off the top of my head.
