I have a lot of ideas what the FS ARG should be.
It may be featured in a small campaign set in the time period of FS2.
It may be featured in updates to existing mods such as Between The Ashes, Inferno, and Blue Planet. Valve did this via updates to Portal in March 2010, so why not one for any?
There is at least one speculation that it may promote my project, Shattered Stars: A Deepness Within, in some form. One may see hints pertaining to the game, but it can also promote other projects. It can also be seen as an effective way to extend not only the FreeSpace universe, but also the universes of other games, such as the UGSF (eight months ago, one user notes there are many Galaxian assets there that could potentially form the basis for the Galaxian/UGSF total-conversion game, namely the UIMS forces).
Anyway, it can be more or less similar to Phoenix.