Ok, since everyone else is giving their suggestions to get more Marks/Dil I'll present mine which I think might have a better chance of getting people excited about these missions again.
As some one who's done boat loads of the STFs and FAs mainly in PUGs (Pick Up Groups) just winning or getting the optional isn't really my goal any more, but doing it in the shortest time possible or not dying is what I'm aiming for personally. So I was thinking why not make this a second level bonus to all these missions?
I'd imagine the devs have info on the average length of time it takes to finish any of their STFs or Fleet Actions, and if not I would think it wouldn't be that hard to track. What if we were take that number and set it as "par" as in golf, a different one for each mission. With that set you could put in rewards depending on how far below par the team finished the mission in, so maybe a small reward for beating it by 1 minutes, a slightly bigger one at 2, etc.
Now here's the interesting part; Make the reward random. So not just more Omega Marks when you bust through Cure Space, but you might end up with say a 100 bonus Fleet Mark token, or Lobi or EC or Dil. They'd have to scale evenly but it would provide a bit of bonus for those teams that work really well and make Skill a factor in rewards.
Would wouldn't have to reward just quickness either. Perhaps put in a reward if every ship lived through the entire mission (healers become a heck of a lot more popular) or even provide individual bonuses (small but still there) for individual leaders of things besides DPS.
I believe this might be a more reasonable option for Cryptic it's not completely undoing the new systems they've put in place, but instead offering a reward for folks to strive for like they used to do with the Borg Tech while rewarding good team work. That's the kind of thing that will make these missions feel like less of a grind and really is in the spirit of the IP. A major point of Star Trek for me was always people of various backgrounds coming together for a common cause to do something better then was done before. I think this system is a step in that direction.
Play Star Trek: Allegiance - my first series in the Foundry