Our idea is endgame content which is specific to your career (Engineering, Science, Tactical). Upon reaching level 51 with your character you will be contacted by Starfleet Command / Klingon High Council with a request for assistance in your field of expertise since you have distinguished yourself in said career field.
These would be a series of missions similar to the featured episode series currently in game.
Tactical Captains would be asked to go under cover and infiltrate the rival faction to gather information regarding the current war. You would be required to bypass computer security with a new type of mini-game. During your espionage you discover there is a new prototype weapon which has been produced. You then have to sneak into the research facility and make off with the weapon.
Science Captains would be asked to research the properties of a new weapon stolen from the rival faction. This might entail complex analysis, visualized & made interactive via a more elaborate (possibly 3D) variation of the anomaly scan mini-game with additional steps with ever increasing difficulty and or complexity. This analysis process might require the captain to visit several locations in an attempt to gather samples of the materials used in its construction in order to test its properties & effects.
Engineering Captains would be asked to reverse engineer a prototype weapon stolen from the enemy faction. This might require you to deconstruct the weapon at the crafting station into its components and fabricate a detailed unique schematic. This might be represented by a new type of complex and engaging mini-game. Finally you would have to build a replica of the weapon & figure out a way to integrate into your faction's starships.
These missions might be independent of each other, with the player receiving either a new weapon with a unique energy type, a shield system which can withstand this new weapon, or both.
Alternatively, and my favorite option, is for the series to require three Captains, one of each career field, to work together to steal, analyze, then reverse engineer the weapon. A Science captain could only receive the mission from a Tactical Captain after he/she has acquired the weapon. An Engineering Captain could only receive the mission from a Science Captain who had analyzed the weapon.
You could have each Captain receive the unique weapon as a mission reward for passing it on to the next career type or you could have all 3 Captains receive the mission reward simultaneously when the Engineer completes the reverse engineered device.