My vote would have to go to the Mirror Universe with Klingon-Cardassian ruled Qo'noS and the Terran Starfleet Academy as locations. With Terran ESD as a boss fight.
And as a pipe dream, I'd totally want to fight Mirror Wesley Crusher and team up with Mirror Dukat only to get double crossed as he takes the position of Chancellor in the KCA. After all, ambition is its own reflection.
Undine (Not Terradome), Klingons (or SF for KDF), Romulans, Cardassians True Way, Terran Empire, Breen... Essentially a couple of STFs for every front.
With everything being cross faction now I'd be surprised if we saw anything of the KDF/SF war in the STFs. You could probably argue away KDF players fighting with the Feds as a house issue but that just seems a little off and I doubt making faction specific STFs would work unfortunately; I've been queuing for STFs almost non stop whilst I'm in game and it's rare that there's more than one other KDF player in there.
This may be true ,but you know what: If Cryptic really thinks that way, they need to end the war. It's stupid having a war and no new missions dealing with it.
I mean, PvP has basically become my favorite part of STO (nothing I ever expected), but considering we're only playing canned encounters in the queues, it doesn't really matter if we have a war going on or more mock battles like FvF is. The faction split seems to cause Cryptic more issues than it is worth.
Next step then would be to bring out the Iconians fully, and have the Romulans, Cardassians (the real ones, not the Trueway) unite with Federation and Klingons in a war against the Iconians and their servants, adding Romulans and Cardassians to the playable factions.
And then we can have STFs vs the Iconians, Fleet Actions and what the heck else.
Of course, this will screw up any lofty aims at territory control modes, but I have serious doubt this will ever be realized anyway, and just halting the story development for the sake of a feature that may never come is stupid.
Maybe they can even have one final STF against the Klingons. Have the Federation and Klingon players figure out that the Klingon Chancellor has been replaced by an Undine (maybe he was one all along), and have them run an STF taking him down. We could basically recycle the Klingon Arc in DS9 (where Sisko et al infiltrated Qo'nos to reveal Gowron as the shapeshifter - only to find out that it was actually Martok that had been replaced.)