Quoted By:
i feel like there's two types of legendaries. the first type is the god beings, the creators and the embodiment of elements. the second type is just extremely rare or strong pokemon which got distorted through myths or seemed godlike to primitive people. maybe there's roosts of articuno up in some remote mountain, or maybe they represent terminarchs. with the powercreep of legendaries i'd definitely go for some retconning at some point, reclassify some of them as just rare pokemon, allow breeding, and even introduce family lines for them.
as for the new ones, you can write it off either as more closely related and almost extinct species the way elephant birds and moas were, or godmons creating weather birds to watch over many different regions with different climates if you want to go the mythology route.