As stated in the Version 2.0 plan, Square Enix has decided that PvP sieges will be performed under the banner of the three Grand Companies. The flaw in this mechanic is that it will pit friend against friend, and segregate players who might otherwise have wanted to play together.

Due to the above, I would suggest that Free Companies (Player-run Companies) be employed instead. The reasons for this are manifold. First of all, it would allow players to stick together despite their choice of faction. Second of all, it would add an element of socialisation to FFXIV whereby the community actually has a geater role to play in the game. Third of all, conquering the PvP fortress would lend the Free Company bragging rights and a sense of relative importance, which is often a key-motivator for MMO players.

I think allowing Free Companies to control the siege would make for an interesting point of conflict on the servers, one which was player-driven, rather than created by the devs.

The downside of course is that it is harder, perhaps, to balance the battlefield for mutiple linkshells and companies. Balancing it around three NPC factions might be easier for the dev team.