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Multiverse theory aside, going by one universe, here is how I see the legends.
Most Mythical Pokes: Unique
Kanto Bird trio: Rare Pokemon, but simply a normal species/not one of a kind.
Heatran: Tricky, but possibly a species considering the dex and the 50/50 gender.
Hoenn and Creation trio: One of a kind.
Regi Trio: Very hard to say, considering they are artificial, and the occurrence of them.
Over all, I think the power of a pokemon determines it's status of a "Species"
The more powerful it is, the more likely it is one of a kind.