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I think the answer is basically luck, because it took me around 10 ultra balls to be able to capture any legendary.
And yeah, the legendaries in D/P are basically the same in levels and what not, since either Dialga or Palkia appears at level 47, opposed to Groudon/Kyogre at level 45.
And after the Pokemon league, the level 70 based Pokemon are about as hard to capture as Rayquaza was.
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