Since you have devoted yourself to this path Chad, a system similar to AO's towers would be perfect. In AO a guild could claim and plant a tower site, and plant turrets/conductors which both aided in the defence of the site and gave the person planting a personal buff (xxx hp/nano pool or other stats equivalent to an extra piece of armour).
Now since Aneu has already proposed that bases be controlled by a guild, why not have slots around that base for mods/enhancements, these items will increase the hp of the shield generators, the damage of the cannons etc and give a buff to the individual who placed the item in the slot, how does 30 endurance 60 cunning 25 power sound for example?
These items would have to be crafted, giving some meaning to the crafting skills, even Artifice, since those cannons gonna need a colour crystal. Now the materials for this new line of crafted goodies could be gained in a number of imaginable ways, personally id say boss lewt from planet bosses, bringing pvp into more areas of the game.
Any way, just 1 idea, with the current state of PvP taking a dump on ones own screen could be considered and improvement.