It's kind of hard to choose but the two I would debate between would be Ho-oh and Lugia. Probably Lugia..but it's your opinion
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Moltres is a legendary Fire and Flying type Pokemon. It does not appear in Pokemon Gold, but may be traded over from a first generation game. In the reboot of Pokemon Gold, Pokemon HeartGold, Moltres is encountered in Mt. Silver.
I don't preferably like legendaries, but Lugia is definitely the best flying type in the onto region
There is Articuno, found in Seafoam Islands, and Delibird, which is only available in SoulSilver