[quote=Sketcher]
The only one without more than one is probably Arceus.
[/quote]

I think there are two separate canons: movie/anime and game. I tend to go with the games, but that's just because I haven't watched the anime since Ash was in Hoenn. In game canon (as far as I know), Ho-oH, Lugia, the Beasts, Mewtwo, Kyogre, Groudon, Rayquaza, the Lake Spirits, Dialga, Palkia, Giratina, Arceus, Darkrai, Cresselia, the three dragons from Unova and the "Musketeers" are all unique (haven't played Gen VI, and probably left some out).

Latinos and Latias didn't get any development in the Hoenn games beyond "go catch them", so I guess using movie canon there is fine. Did they reproduce in that movie they were in?