>>34799303There are definitely legends that go both ways. Most of the lesser legendaries (600 BST and below) certainly seem like there'd be multiple of them (Latias in particular are even said to form herds) and a few of the stronger ones seem like they could be a multi-member species (Lugia and Ho-Oh seem likely to be this, to me anyway). However, those with more fleshed out backstories like the Tao Trio are definitely single-member species, at least in the world we know (if you believe that whole "Kyurem may be an alien" thing, anyway).
For me, my autistic head canon is that the Tapu were originally some kind of shamans or the like for each of the islands, and some event caused them to incarnate as Pokemon connected to the lands they lived on, making them unique. 
