This whole thing has brought me to an interesting theory: I noticed that there always seems to be a connection between the "pixies" and the "leading" uber of the Gen. It's always that the pixies have powers that would enable you to get to the superlegendaries under normal circumstances (while in the games, the superlegendaries always come to you).
For Gen 1, this is obvious: To get to the clone Mewtwo, you first needed an original, Mew.
In Gen 2, it is implied (and told to you by many people) that Ho-oh and Lugia were the guardian of the ancient world but left humanity a long time ago. Celebi can travel to the past where they still were reachable (for normal humans).
In Gen 3, especially the story and the pokedex imply, that Groudon, Kyogre and Rayquaza used to change the way of nature to adjust it for mankind. See the pokedex:
"Groudon has the power to scatter rain clouds and make water evaporate with light and heat. It came as a savior to people who had been suffering from terrible
floods. Kyogre has the power to create massive rain clouds that cover the entire sky and bring about torrential
downpours. This Pokémon saved people who were suffering from droughts." The only power which possibly allows you to avert natural catastrophes is... wishing. =)
And in Gen 4, we basically face all the creators of the universe, the supreme one being Arceus. So how can we reach the creator? By showing gratitude for the creation. That's what Shaymin is for. It even has the powers go against all odds (by flying and having enormous luck xD).
So, I'd say we can conclude that if our little V-Head actually is this gen's pixie, it probably follows a similar pattern. Being a "phantom", I can see it having something to do with reincarnation, as this is a way to achieve the point of balance between Yin and Yang. But that last one is just a guess, obviously. ^^