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Legendaries only being “one of a kind” didn’t start until Gen 3 when Groudon and Kyogre were attributed with actually creating the planet Earth as we know it. Then the Gen 4 legendaries completely jumped the shark with being gods themselves. Although the legendaries in Gens 1 and 2 were said to be extremely rare (I believe the three legendary birds were called “gods” by the Collector villain in the second movie), the only one that was actually known to be completely one of a kind was Mewtwo himself, who was artificially created. Even so, it’s been explained that Mewtwo could simply be cloned again.
