1.) Mini-Episodes based in the queue system.
Introduce the form of a mini-storyline that is not only based in the central PVE content, but that also includes some PvP content. For players to achieve the end-goal, they not only have to complete the PvE content, but also the PvP. Use the form of simple decision-outcome scenarios the storyline would unfold based on the outcome of the missions as well as the PvP. e.g. The Klingon Defence force is in pursuit of a dangerous Ferengi Marauder close to the Neutral Zone. Unbeknownst to the Klingon ships, the Ferengi Captain has already made contact with Starfleet pleading for sanctuary. The Klingon ships and Starfleet encounter each other and before PvP clicks off a brief vocalised on-screen ensues describing the incident. The outcome of the PvP battle will determine the next phase of the scenario, e.g. does the Ferengi manage to escape the Klingons and make his way to one of the Federation Outposts? Are the Klingons forced to retreat and do the Starfleet officers have sufficient mandate to pursue the Klingons? In this way the game can gain a more dimensional feel to it.
2.) Merchantmen and Marauders.
Once the player has reached a certain point in the game, based on experience, or accolades or items bought and sold on the exchange, they decide whether they wish to become less-faction specific and take-on the role of Merchantmen or Marauders. Although their primary faction remains the same they would become a neutral faction that could play on both sides. Perhaps they could select a new race like the Ferengi and gain access to the Ferengi Marauders etc. What would their role be? Well something along the lines of crafting, except there would be certain wormholes where only they may go to explore and complete "acquisition" missions. The items found on these dailies could then be crafted into rare items with special abilities or unique skills. Although they would not gain use of the items which can only be sold, after creating a certain number of trade contracts, they themselves would acquire totally unique weapons and such.
3.) Ships Computer generated PvE Content
This goes without saying, and would give character to ships and players.
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Comments
The thought was pvp linked missions.
Two different (unknown to each other) pvp players who are competing for the same planetary species to contact, subjigate, etc. Klink vs Fed or a house battle for the honor.
It could be done at random when two oppossed players try to enter a planetary system, when a player enters a system with an enemy player already in it (could be started by the ol' " Captain we are being attacked!! Beam back" or just controled by the server where it matches opponents together.
After the combat on ground or in space (could be a choice option) the winner gets the exploration, diplomancy, etc mission to run and acrues honor or prestige for thier faction.
PvP storyline missions - its an idea - may be possible.