Some ideas I had for the game:
1) Artifacts
A planet has a certain chance to contains a artifact, either a component you can replicate and produce yourself. or maybe a single component that you only have ONE off.
A ship can scan a planet (takes time depending on sensor strength and crew experience), and detect the artifact, which can then be retrieved by an away team.
2) Carrier ships
These would be HUGE ships (obviously not cannon) that require maxed out tech, and a large starsystem dedicated entirely to industry just to build.
Carriers would have extreme armor, hitpoints and shields, and the firepower of a handfull of soverign class ships.
Carriers would be able to build, repair, refit and refuel a whole fleet of ships. And would be like a moveable starbase/shipyard. The carrier would have an great deuterium storage capacity, and would be able to process raw materials from nebulas (deuterium fuel) and ore (used to build / repair ships).
Carriers would become an important part of the endgame of each game. If no carriers are implemented, Starbases will serve the same purpose (but of course be stationary, or have a speed of 0.1 or something :)
2b)
The Carrier could even be so big that it had to be built in stages, and several users in a faction would have to join together and build the components required to get the ship done in a reasonable time.
3) Economy
MAYBE after the first release, I would implement economy.
Latinum is the currency.
There is a open marken where everyone (within the same faction) can post sell orders and buy orders.
AI will generate buy orders for the ferengi or minor races, so that users can gain some latinum.
Users could be able to buy/sell ore. dilithium, ships, starbases and maybe even starsystems.
4) Open for all game mode
Instead of just faction vs. faction.
Players would form alliances (guilds), trade would be possible between ANYONE, techs could be sold, as well as faction specific ships.
These are just ideas, but I would very much appreciate some feedback :)