This is an idea I have "borrowed" from America's Army.
When we are PvPing, we always face the same enemies, I mean, Fed or Klink...
Assuming that the PvP, inside the game, is just a warfare simulation, is it not logical to think, that being in war against several races, we will be practicing against the same targets over and over again, so here is my idea.
The enemy team could be or not be skinned as the race it belongs, it can look different, for example cardassians, or orions or dominion (for Feds) or romulans and terran empire in the case of klingons or any other invented race with cloaking device technology (this is purely for compatibility purposes).
So basically, you will see yourself and your team, as usual, klink or fed, but the other team may or may not look as originally.
Off course, ship sizes and types will be respected, for example, you wont be a defiant with the skin of a dederidex.
And the powers will be the same, this is just something totally cosmetic, just to add flavor to the PvP.
I'm going to have to say that is a bad idea. If you want to fight Klingons just que for FvK we are always needing some Feds to fight. FvF really never should have offered the same rewards as FvK in that it is supposed to be nothing more than a "simulation". The real war is supposed to be FvK and if anything should be promoted more by Cryptic.