1) Meaningful ship/star base classes: Each class should have a distinctive tech tree with unique equipment for that class. For example a destroyer should not be able to use battelship-sized lasers, and while a battleship could use the smaller equipment from a destroyer/cruiser, there should be some sort of efficiency penalty. This change would go a long way in making ship design (and research) far more interesting with meaningful choices.
2) The private sector needs a voice: the AI-controlled private sector is the most fascinating aspect of DW, but it needs more development. For example, I would love to receive missions from various NPC corporations along the lines of designing a special freighter for them, or patrolling a hostile sector to keep cor[ ships safe from pirates, or even a request to go to war with a particular alien empire so as to get access to its luxury resources. Failure to complete these missions would have a negative impact on the players economy, and could even result in a strike or work stoppage, setting off a potential civil war even?
3) When ships are added to fleets, they need to be grouped together into one unit. In other words, I am tired of fleets arriving in combat by drips and drabs. Rather, all ships in a fleet should move as a single unit in a specified formation (with speed set according to the slowest ship class).
Bonus Suggestion 4: see here: http://www.matrixgames.com/forums/tm.asp?m=3130727 for suggestions on creating a more living universe.
These three suggestions sound perfect. Private sector missions would be a great addition, but as long as we can toggle them on and off.
I mentioned long time ago fleet formations. I would love to have them in this game since large scale battles become such a mess.
Maybe they could introduce custom formations in which you could assign positions to ships: eg. keep carriers in the back with large, slow but long range capitals; then in middle have damage soaking, heavily shielded/armoured tanks; and up front have smaller, fast hit and run ships which would harras enemies.
Of course you could make up number of other formations to suit your playstyle.
Also, I don't know if this would be too difficult, but maybe Elliot could make more use of firing arcs on weapons. This way flanking and turning cirlces would have more importance.