So why did I mention MMOs, you ask (only in my mind, anyways... *shifty eyes*)? Well, the idea involves using things that already exist in them in a way that hasn't been really thought of yet.
Well, we already have instanced content. For the uninformed (and anyone reading this shouldn't be), instanced content is pretty much where the game servers create an additional "instance" of an existing area that is seperate from the rest of the game world and usable by only the players within it. The reason for this is so that more players can experience more content without having to compete against other players to do so. It is typically (but not always) used with storyline or chain-quest areas, and are almost always very large and involved (for various reasons).
Then, of course, we have PvP. IE, the videogame answer to people's need to kick the crap out of eachother, and it takes different forms depending on the type of game its used in. No real need to explain it beyond that.
So my new, supermegaultracrazy idea, is to take both of these elements and find a way to smush them together. But MMOs that have PvP already have instanced areas designed expressly for PvP. How does this differ from those? Well the difference is purpose. Instanced PvP areas are basically similar to control-point style maps in online FPS's, with the basic idea revolving around killing opponents in order to get to and takeover said control points. While the areas could easily be repurposed into standard PvE content, they are purpose built specifically for handling a specific kind of PvP battle, which is almost always the big-freaken'-melee (even if players are smart enough to avoid that).
Now, when someone says the word "instance" in MMO terms, they usually refer to the first definition (and use a different term for PvP instances), which takes the form of a semi-linear dungeon. This is where I think PvP can be added. Just about all MMOs that have any form of large-scale PvP involve dev-created opposing factions. As well, in those games the world and quest lines are designed to bring those players into conflict. So why can't the devs find ways to bring these two things together in more interesting ways?
That's the idea. Bring dungeon instances and PvP together. This is still hypothetical, but since both factions are opposed, create an instance that plays to that. Have players from the two factions have quests that require them to enter instance. When entering, faction A starts at one entrance, faction B at another. The players run along doing their quests on seperate paths, but the paths will intersect at several points, designed around forcing the players into conflict. But then, make a quest requiring the conflict, and if there are no players, spawn higher level enemies in the room instead, to fulfill the quest requirement.
So when players are killed, they should respawn within the instance. But then, this could potentially lead to players griefing players on the other side. Well, the only real solution to something like that isn't something that will be popular. Since a quest requires defeating enemies (bots or opposing players), then "shove" them out of the chokepoint as soon as the reqs are met. And then there's the problem of bringing along a high-level friend, or even a full group of them, well that's only really solvable by the infamous thing known as level-caps. To keep from inconveniencing said high-level players, have a simple equipment balancing system introduced alongside the level-capping.
Admittedly, this is just the basic idea. Hell, I spent more time building to it than stating the idea itself. Ohwell, take it for what you will.