If you're looking for a high leveled Pokémon you can catch in-game and use in battle, I'd recommend Lv. 70 Rayquaza (caught at the Sky Pillar) or Deoxys Lv. 80 (caught in space shortly after catching Rayquaza). These are both legendary Pokemon with good stats encountered at a high level, so they should be good for in-game teams. If you have a masterball, I'd use it on Deoxys. If you still need more powerful Pokémon, don't forget that you can have Groudon/Kyogre can Primal Reverse and another Pokémon Mega Evolve in the same battle, if that helps. For Mega Evolving Pokémon, I'd recommend Lucario, Salamence, or the Mega Evolution of a final evolution starter Pokémon from any region (the Kanto ones are pretty useful, if you have XY). I don't know what levels they're encountered at in the game, but these are some powerful Pokémon and can really make a difference when you get stuck.
