So capture and holding of territory is on the cards for STO. I do not know what cryptic has planned but I decided to put an idea out there. Some people will hate this others who want a thrill will love it.
So my idea for territory capture and hold is a bit like eve. Every faction should have their own " Safe Areas" were pve players can do missions etc.Enemy factions can cross the border of your faction but are met by strong npc ship patrols that can push them back out to their own space. Every faction has borders along their territory. If you decide to cross these borders then you enter a territory control zone much like pvp. You are open to attack from other players of the opposite faction and the missions beyond the borders are harder, more dangerous in that you could lose your ship and more rewarding if you complete them.
In these territory capturing zones you can attack enemy players and bored their ships, steal the loot in their invetory and if your real good either capture their ship for parts or completely destroying it.
If your a real risk taker you will cross the borders of the enemy faction and get met by heavy npc resistance. the npc patrols will protect their factions space and spawn anywhere theirs an enemy intrution.
Ive tried explaining this the best I could, found it hard to explain so ask me questions if you dont understand. Im off to work now so ill add more later.