Legendaries

Latios: I think this needs clarifying...
True Legendaries, also called Big Legendaries:
Hybrids considered true legendaries:
Mewtwo, Lugia, Ho-oh, Kyogre, Groundon, Rayquaza, Deoxys, Dialga, Palkia, Giratina, Regigigas, Arceus, Reshiram, Xekrom, Kyurem, Xerneas, Yveltal, Zygarde (Note: Some of them may not have been born yet)

Unique characteristics:
They are immensely powerful and biologically immortal. While they can, technically, be killed (except for the truly immortal Xerneas) it would require a ridiculous amount of firepower, possibly up to a few nukes. Many of them consider this world to be as fragile as cardboard and just as boring, and have such hidden away in secluded locations to either hibernate or pursue little hobbies away from the world. All of them keep their species' name as their true name.
A legendary is actually just a regular human who was "born lucky". Some time during conception or pregnancy, a truly incredible amount of Aura flooded into a legendary's body by random chance, giving them the form and powers they have in life. (As a side note, hybrids' children are technically born human, but during conception so much Aura is passed from the couple to the mother's womb that they're almost always born a hybrid.)
Additionally, the amount of Aura they possess in simply being alive prevents any other hybrids from being born the same species, so they remain unique until death.

Small Legendaries, also called Unique Hybrids:
Hybrids considered small legendaries: Articuno, Zapdos, Moltres, Mew, Raikou, Entei, Suicune, Celebi, Regirock, Regice, Registeel, Latias, Latios,  Jirachi, Uxie, Mesprit, Azelf, Heatran, Cresselia, Phione(?), Manaphy, Darkrai, Shaymin, Victini, Cobalion, Virizion, Terrakion, Tornadus, Thundurus, Landorus, Keldeo, Meloetta, Genesect, Diancie, Hoopa, Volcanion (Note: Some may not have been born yet, and Genesect will be manufactured, not born)

Unique characteristics:
They are biologically immortal, have abilities unique to them, and have enough Aura to prevent another of their species from being born. Other than being more powerful by default than normal hybrids, they're... pretty normal. They typically live in society as much as it pleases them (which is a lot more than true legendaries).
Like true legendaries, small legendaries were "born lucky", having far more Aura fill their being than a typical human.

Question; as has been shown in-universe, there can be multiple Shaymin and Phione. Could some of the 'small' legendaries be too small to be fully unique? So, Shaymin, Phione, (I think) the Regis, and (I think) the Latis?

And also for the smalls, maybe not biologically immortal... probably just ridiculously long-lived. For some reason I can picture an old wise Ho-Oh sipping tea in some hut and nodding sagely as time passes, but... not... a Phione...

You bring up some excellent points. Still, some of them still seem like they'd be immortal, like Latios and Latias and the legendary birds... hmm... maybe I need a hierarchy of sorts?
Edit: On second thought, keeping them all long-lived is a good idea. That way it can vary from a shorter-lived Phione to a reasonably ancient Cobalion, which makes more sense, I hope.