I'd like to see an undine rep system. With items like biological undine consoles and equipment. Maybe one of the passive abilities you get is a resistance to borg tech. Also, a rep for the dominion and breen could be interesting.
I would like to see a Fed or KDF rep. So you can get some nice equipment with your own faction. The Romulans get one with the New Romulus Rep. The Feds can get Phaser, photon, quantum upgrades. While the KDF can get disruptor, and photons upgrades. There is a lot that can be done with this.
The Rep is totally optional. Unless you want to see the story line. Then you can do it once, and don't do it again. To me these are easy and not tasking to do. Unlike some games you have to log on and do it each day until your done. Now that gets old very fast. Where this one, I build up points. Just log on to turn in and get another going. Get on another character to level up. Or stay and grind dil or other stuff in the meantime. This is one of the easiest Rep systems to do, and I'm loving it.
How about Starfleet Core of Engineers/ KDF Fortification Division/ Republic Reconstruction Command?
Puts the AEGIS set (with a new Mk 12 edition that's a little nastier) back into circulation, and it makes sense as a 'the mad engineers trust you not to blow up their new toys' branch replacement for Memory Alpha Crafting.
Uses a lot of particle traces and data samples, that sort of thing. Gets them flowing again.