The hardest issues for PvP-only Territory Control would be:
Balance (population numbers would never be equal, i.e there will never be more KDF than FED and certainly never more Cardassian than FED - sad but true).
Appeal (PvP is a niche within the MMO genre - most people chose not to participate, even if compelling).
Risk v. Reward (there needs to be some sense of accomplishment - and loss)
balance (population) ; I am working an an idea for pvp missions that I am going to submit for review, but the basic premise was two players fighting over the right to do a single contact mission. In the event of no rivals, the mission would go to first faction on site. Same thing may work here.
appeal ; The ability to brag about one's exploits and having control of sector areas? This is a toughie.
Risk vs. Reward; Risk losing control of the sector and having to retake it or irsk not having the tactical advantage. Reward being some sort of bonus for controlling "x" % of said sector.
I still think the idea has merit, but will require a true braintrust to figure out how to do it, and frankly I don't trust my brain today. ( its been plotting against me, I've seen it)
Then small sattelites are added to defend the outpost etc.
So in the end it would take more attackers to engage the outpost over the course of time.
However I'd propose for example if the Donatu and Archanis sectors were used as places for the PvP zones and the outposts were fortified over time, the materiel needed to make those upgrades would need to be transported to the controlled sectors.
So there would be convoys of freighters with their escorts ferrying the materials to the PvP zones.
For example there could be one of more convoys moving into the PvP zones over the course of time, depending on the amount of grid sections a certain faction controls at a given time.
And only when a convoy actually reaches its destination, one of the controlled grid sections is reinforced with new defenses.
This would give the opposing faction time to attack and destroy those convoys, while the defending group, that waits for those vital convoys to reach the front lines, would have to defend them unti they reach the outpost.
Like Martok escorted a convoy in DS9:"Sons and Daughters" http://memory-alpha.org/wiki/Klingon_cargo_vessel
The Klingons could get regular convoys coming from the Gandola Station while Starfleet gets its convoys from K7.
The theory is that when for example the Federation controls several more sectors that the Klingons, the Federation would have a lot more convoys coming in to help fortify those controlled sectors, while the Klingons would have a wide range of juicy convoys they can blow to bits, while the Federation would only have a limited number of ships at their disposal to escort those same convoys.
Now the interesting part is that when a convoy is not defended by players, it could still be defended by determined high-level AI ships, so it would still not be a simple cake-walk for an attacker to take out the convoy, but it is certainly true that the AI can not be as good as a seasoned player.
When a player decides to escort the convoy, the AI is replaced by that player and only a limited number of players can escort a convoy(just to say an number:4), just like ony a limited number of players can engage a convoy(let's say 5) and the convoy is only vulnerable for a limited abount of time (say 5 Minutes).
So when you bother to engege a convoy you can never be sure whether it will be defended by mister computer or by a real player, but it might still be interesting for some PVE players to try and attack a convoy and try to destroy it in those precious few minutes it is possible, even if those players would never want to get involved into a major PVP war.
I like some of the ideas presented here, they are certianly better than the existing system. However, unless i missed it here somewhere. Do not understand barriers in space between faction borders. Open PvP, means open PvP,
if a Fed or Klingon fleet bans together and attacks point A on a map. Then that point should become contested territtory and anyone entering shold be ready to PvP. If I take my BoP to Memory Alpha and get caught trying to sneak in and kill a sentry ship, then I should be flaged for PvP and any number of eager young Feds should have the shot to blow me to Stovokor. It would certianly be more entertaining than sitting in my two sectors, fighting a defensive war, waiting for PvP ques, when Klingons are supposed to be on the offensive? Whats the plan for Romulans, coupe that faction up to 1 sector because they have apparently lost alot of territory?