With regards to tying it into the normal day to day gameplay... I could see the devs making Nexus a place for factions to fight over in order to actually get a chance to conquer the island. Have factions fight over who gets to take it and then have the winner try and defend the island from another invading faction (Which of the other two factions get to invade would also need to be decided).
Basicly just have control of the island be about two factions fighting it out, not a threesome as we always have now.
Also glad to see some new indoor areas, hopefully we will be seeing more of then outside of the Nexus.