I feel right now like there are very limited ways of obtaining Fleet Marks (not so much Dilithium, but other options are always great) in STO, so I'm gonna cut to the chase and throw some ideas out there.
I really like the featured episodes and replay them more than any other missions. Why not give VAs Fleet Marks and/or Dilithium for playing them, in place of skill points? Something like X Expertise with a choice between 15 Fleet Marks per mission OR 480 Dilithium per mission.
I love these. They're like mini-Fleet Actions, purely space combat, great for soloing (and we'd all love a little with that seeing how much dead weight there can be in a fleet action).
Instead of rewarding us with Skill Points for completing a patrol at VA, reward us 10 Fleet Marks OR the choice of 480(?) Dilithium.
Give us a Daily/Repeatable mission to explore 2 or 3 systems at a time, that we can turn in for 1440 Dilithium OR 30 Fleet Marks.