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Rayquaza
Arceus the alpha Pokemon, it created pokemonand its base stats is the highest over any other Pokemon, Its the best Pokemon on paper, but when you play with it its not the BEST Pokemon out there. If you level all Pokemon to level 100 then Arceus would be the best, at level 100 it learns the move jugment. Also, if you catch a high level Pokemon, like a level 70 lugia, then level it up to 100, it wont be as stroung as if you got a level 20 lugia and level it up to 100, this is because the Pokemon earn more stats when you train them and not as much in the wild. So its best to get slightly lower level Pokemon, not the highest. Now, the best Pokemon in Pokemon hh and ss. This is only the best one avaulable to catch, without cheats or trading. The best Pokemon is probobly Lugia.
There isn't one Pokemon that is "better" than the others; how good they are depends on their stats, level, moves, and how you use them.
depends if its night then dusk balls if its the heart gold one then level and nest balls when you train alot
best weapons depend on your level.