I would like to propose a game-wide reward revamp. Specifically, give people multiple choices for all mission rewards. For example, when completing a mission you could choose one of the following:
A piece of level appropriate gear
An amount of dilithium
An amount of fleet marks
An amount of reputation(if the mission involves Rom or Borg)
Such a system would give all existing content a very high replay value and give players a much larger selection of things to do to get the specific type of reward they want rather than having to repeat the same missions over and over again.