In a free for all battle with all Pokémon: Magikarp. Seriously. Every Pokémon would fight together again Lugia, Mewtwo, Groudon, etc. untill they are all down. All the remaining Pokémon keep fighting against the strongest Pokémon left untill the only Pokémon remaining are Feebas, Caterpie, Weedle, Wurmple, Metapod, Kakuna, Cascoon, Silcoon and off course Magikarp. Weedle uses Poison Sting on Feebas and poisens it. Feebas then slaughters everyone with Surf, except for Magikarp against who it is Not Very Effective. Both are very much weakened. Then Magikarp, being the fastest of the two, finishes it with a Flail.
But if all Pokémon won't team up against specific Pokémon, either Lugia or Metagross will win. Lugia is the single best tank ever. It survives every hit and heals away all damage with Recover and blasts everybody else away with Aero Blast.
Or Metagross, Slowking and Alakazam, being the three smartest Pokémon of all, stand on the side and wait untill the battle is over. After blasting away the last survivor, only those three surive. Metagross used Meteor Mash. Alakazam fainted. Metagross used Earthquake. Slowking fainted.