Cryptic could introduce a maximum daily or weekly allotment of each mark type that can only be earned through official episode replay. If you don't earn your allotment, then it does not roll over, but you can decide when and what to run to optimize your game experience. This would need to be balanced in some way so as to avoid people abusing the shorter Borg/Undine & Romulan missions. Perhaps by only being rewarded for running them once. There are plenty of missions for each faction.

Some advantages:

• Additional, customizable sources of mark generation
• Re-use of existing developed content to reduce costs
• Possibility to throw in a few random encounters inside these missions by way of a wrapper mission
• Makes old content relevant
• Possibility to introduce a bonus events for additional marks
• ??????
• PROFIT!!!