The Two Pokemon Of The Elements:

When going after the legendary representing the team of your game (Team Aqua or Team Magma), bring about 30 Ultra Balls, quite a few Revives, and at least a level 50 Pokemon. The Pokemon will be at level 45, and will be extremely difficult to catch. The only sure way to catch it is if you bring a Pokemon with a move that will freeze or paralyze it. Try as hard as you can not to kill it, but get it down to a red zone so far down that you can barely see it. Then, go mad throwing Ultra Balls at it. Do not use other Pokeballs. The will help greatly against the Elite Four and the final Gym leader.