There are multiple Mew and Celebi; the Mews in movies 1 and 8, as well as the Celebis in movies 4 and 13, are different individuals. Extremelly elusive species that are very powerful, as strong as things like Dragonite or Tyranitar.
The legendary birds and beasts also seem to not be that unique, just elusive. There are several sets of Regis. Latis have a breeding population (Pokemon that do not breed are just unable to breed in captivity). Heatran is functionally a pseudo-legendary that has no preevolutions and does not breed in captivity. There are multiple Darkrai, and Cresselia, well, Palmer has one.
Phione are normal Pokemon, maybe made by a Manaphy to assist him, in a way similar to eusocial insects, with Manaphy as hive queen.
Deoxys, it is always associated to being a pair of them, but it is mostly a mutation that happened near Earth.
Lugia and Ho-Oh, I'd say one or two, if we count the Orre ones. May reproduce. Mewtwo is a single individual until proven otherwise (Mew happens to be prolific, after all).
Weather Trio, single individual. Creation Trio, single individual until arceus made more. Lake Trio, single individuals. Arceus, one.
By the way, 5th gen stuff starts on March, right?