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I'm not too sure on my favorite legendary for Hoenn, but if I had to choose, it would have to be Latias. She's simply adorable in Pokemon Heroes, and she's Red.
Second would either have to me Rayquaza or Jirachi, I guess.
It's hard to choose between Kyogre and Latios for me. I like both of them but because of its superior strength I would probably have to put Kyogre over Latios.