no not really . . .
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yes there are there is the cloning glitch at the battle tower which clones your Pokemon and you get it back at the same lvel and every thing but you have 2 of them (this glitch can delete Pokemon from the game just a warning).
You can only use the hack, glitch, or Gameshark. I don't know any other way.
rayquza. He's in the sky pillar
Any Pokemon that is not a legendary Pokemon can be bred. An example of a legendary Pokemon would be Heatran, or Ho-oh. Any normal Pokemon, like pikachu, can be bred.
I don't think you can refight any legendary Pokemon except the wandering dogs.