Borrowed the idea from Mass Effect 2, so forgive me if it might sound a bit cheap but...
A mission, or perhaps even a full episode, that brings us to the crash site of Enterprise-D would be a cool addition to the game I think.
Possible plots might involve
- Vsiting the place to scan for, and/or contain dangerous fallout by using the omni-potent F key (preferably done at a low-ish lvl, Starfleet HQ probably wouldn't send a star cruiser on this)
- Crash survivors and family members of the fallen gather for a memorial ceremony. Your job is to A: represent Starfleet, and B: protect this from the Big Bad. Then, something Completely Unexpected happens... (could be done at higher lvl, this is an important occation and high profile representation from Starflet is expected. And since your tier 5 ship is already starting to build a legend of it's own, and already conviniently in the area...)
I'm sure you all can come up with more and/or better. Feel free to share. This is after all intended to explore ideas to improve the game.