I too want to see more of 1v1, 2v2, or 3v3 PvP. Because you are more about the individual's PvP skills than groups such as premades or PvP fleets.
My PvP Zone Ideas:
Basic Open PvP Zone - Which is basically a large empty zone which PvP can take place, which a population cap of 30. In which Cryptic could add various hiding spots for Federation ships that could hide a player (such as "behind the moon", "above the magnetic pole", nebulas, or asteroids fields.
Free Rank Open PvP: Where any rank can PvP, but players are still either Federation or Klingon. So a Negh'var can go pick on a Miranda or a 2 B'rels going toe to toe with an Excelsior. (Zone would be limited to a population cap of 10).
Territorial PvP (Space): Simlar to Capture and Hold, but on a greater scale.
Where territory is controlled by capturing points. Where each point is at equal distances on the far corners of the map. And to capture the point, you have to beam on board the station and accomplish certain tasks to gain control. So PvP can take place in Space or on the station.
Population limits set to either 10 or 20, to ensure strategy.
Station Defenders can have access to base defenses to delay attackers.
Territorial PvP (Planetary):
Space Zones are Open PvP of unlimited population and open to all ranks with various hiding spots in orbit.
Players can beam down, to safe locations to respective bases. Then they can gear up and then proceed to their choice of battlefields. For instance:
To the North can be a Swamp Battlefield.
To the South can be a Mountainous Battlefield.
And players must make their way to the center (between the two bases), in which players fight over control over a central base, NPC village, or Ruins. Where whomever wins, can gain control of the planet.
PvEvP - Battle for the Loot: Similar to the above, instead of gaining control of a world, players battle for rights to access to a PvE dungeon, where you go to battle a Boss-level opponent for the chance to acqure a rare unique drop.
PvEvP - Antagonists: Where two players on opposite sides are sent on a PvE mission (can be storyline driven), where they act as each other's antagonist.
For instance a Federation player might be tasked to escort a Freighter to X, while a Klingon player has to either board or destroy that frieghter.
I must admit that these are some interesting Ideas.