This is only a suggestion but what I would propose with STF's since I know the way they have it setup for stf's is a proven success as far as how they new drops work and such on other MMO's but one of the things I wanted to suggest because fighting borg and same 3 STF's all the time can get super boring. What I would like to see is these featured episodes when they hit the final episode leading up to a branch of new STF's so you can do this grind but have some variety on what you are fighting. This I think would work really good starting off on the Romulan/Reman series since it leaves you hanging on the result of iconians and Sela. I know there are still some Borg ones planned but there will come a time when STO players will get burnt out on this borg trip.
I would like to see FE series on the following topics:
1] A continuation of the Sela/Iconian story arc.
2] Something centred around DS9, the wormhole and the Gamma Quadrant.
3] An end to the Klingon War (I'm really bored of it now, aren't you?)
4] A Betazed-set story. USS Titan? Riker and Troi? Hint hint? Can Cryptic craft the ultimate tribute to our dearly missed Majel?
5] A fully fledged time travel story set on Earth - it would be awesome to take your crew to 1986 San Francisco and parallel the events of ST4.
6] Bring back the Suliban!
7] A story based around a natural threat instead of an established enemy, much in the vein of the whale-spaceprobe-thing.