Well, neither did Manaphy when it was first revealed to be honest, but it's still a Legendary Pokemon. There are tons of others that are small like Meloetta and Kerudio, yet are still classified as being Legendary Pokemon. Contrary to popular belief, size doesn't matter, at least not when it comes to classifying Legendary Pokemon :x
While Manaphy is a Legendary Pokemon, there is more than one classification than just Legendary. Manaphy is in the classification of "Phantom Pokemon", like Mew, Celebi, Jirachi, and Shaymin. Each was made with powers unlike the main legendaries of a game, but with enough strategic power to defeat them. There was 1 for each generation, Mew for the 1st, Celebi for the 2nd, Jirachi for the 3rd, Manaphy for the 4th, and Shaymin, for the Pokemon that dont really live in a "region",but are just extras after the Sinnoh Dex, which I call the "Non-Existant" Pokemon.
Mirage Pokemon are those that serve under a Legendary Pokemon such as: Articuno, Moltres, Zapdos= Lugia, Entei, Raikou, and Suicune= Ho-oh, Regirock, Regice, Registeel, serve Regigigas, while Rayquaza, Kyogre, and Groudon were said to (and this is just speculation) serve under Latias and Latios, who were mysteriously linked to the orbs of that region, the Soul Dew, the Red Orb (Latios due to the color of his delta sign), and the Blue Orb (Latias, for the same reason), while the Jade Orb was just a man-made product of trying to make an orb to control Rayquaza, and then there is Mesprit, Uxie, and Azelf, who serve under one deity at a time, them being Dialga and Palkia, yet while they have nothing to do with Giratina, they use that world as a type of protection against ours.
Then lastly there is the Mythical Pokemon, being, the Unown, Lugia, Ho-oh, Rayquaza, Kyogre, Groudon, Dialga, Palkia, and Giratina.
The true legendary pokemon would just be Latias, Latios, the "Non-Existant" Legendaries in Sinnoh, and Arceus.
Mewtwo and Deoxys are not "real" pokemon for they were literally "made" into what they are, Mewtwo by men, and Deoxys by our atmosphere.
Not trying to be mean or anything if it sounds like I am, just putting up some interesting information.