Of course, there are restrictions to using the free version. Vita players will be limited to only certain shared areas with PC players and will also be unable to play the game in any sort of offline mode. Players will also need to swap memory cards to change accounts, as the free version is tied to the PSN account information stored on a memory card.
Will this be true of the Western version as well? It's unknown, as Sega has yet to officially announce that Phantasy Star Online 2 will be on the Vita in the US. Keep your eyes peeled as the game gets closer to its Japanese release and more information comes out about localization.