Okay, I've posted previous models for PvP that offer players a category of decisions that go beyond the tactical aspect of battles, and more toward the level of operations and strategy. There have been several thoughtful players who have presented models for PvP that point in this direction, and all of them require either a large static map, or sectors open to PvP. On these maps would be the locations of resources and bases that would be central to a faction's survival, yet numerous and dispersed enough to provide some redundancy as well. The result would require thinking that moved away from the plodding steps of battle and more toward the conduct of battles through operations, directed by a unified strategy.
Having said that, much of my previous thinking was grounded on the assumption that there would be an intrinsic balance between factions, numerically speaking. Why I assumed this was very silly, since even then it was pretty well known where the massive proportion of players would reside: the UFP. As it stands now, I believe the disparity between the Klingon faction and the UFP faction is quite literally 1:10, respectively. Any idea of balance must be tossed out the window with this sort of yawning gap.
This definitely requires a change in the PvP model. With a 10:1 advantage in numbers, the Federation could overrun the Klingon faction at will. This sort of predicament would be too oppressive for Klingon players and likely result in a reduction of the faction's active population.
Thankfully, the Star Trek universe provides an answer. Since the Federation never initiates a war, it matters little for there to be a Klingon side to the PvP map. All that matters is for there to be a Federation side. In fact, the map only really needs to cover the Federation up to the Klingon border. This will put the Federation on the strategic defensive, and the Klingons will be the invaders.
As the Romulans are introduced, their border with the Federation will be incorporated, and they will also invade the UFP. The same goes for all other hostile factions introduced to the game.
As special events, Cryptic could create maps of the Klingon Empire and allow the Feds to conduct a limited counteroffensive into Klingon territory. Or the Romulan Star Empire. Or whoever else.
Given the overwhelming popularity of the Feds, their numerical superiority is likely assured. By limiting the Federation to the defensive, those numbers will only serve to repel attacks, allowing the numerically inferior Klingons some degree of freedom to range free and wide. The Klingons may never really hope to win a war, but at least they can be satisfied in knowing they are taking it to the Federation. For the UFP's sake, being on the defensive is in keeping with the principles of the Federation, easily explaining the gaming restriction.