First, since my days of beta testing and modding days of Space Empires IV and V I have not been this excited about a 4x space strategy game. I bought the original and expansion shortly before the holidays and have not played a single PC game other than DW since then - I even received Fallout: New Vegas for Christmas but it is still sitting on the side of my desk in a wrapper underneath all my handwritten notes and charts I have made while playing my first game of DW. Kudos to the developers for making what I hope will be a classic for many years to come.
I am sure most of these have been mentioned in some form or another, but my hope is that the ones that are repeated will garner higher attention due to popularity.
(1) [DECREASE MICROMANAGEMENT - RALLY POINTS] Almost every single strategy game (turn-based and real-time) contain these since they help reduce the number of repeated commands mid/late game (good examples - Space Empires V, GalCiv 2, etc.). Optimally, you would create these by right-clicking on a set point in space or an object (a/k/a fleet or planet) and then be offered an edit box to name them. Once created you should also be able to bring up a listbox of current rally points and edit them rename them, etc. (similar to the Fleets screen). Finally, you should be utilize the rally points when you (1) right-click a ship and give it a move order (the list of rally points should appear similar to the assign fleet interface), and (2) in the shipyard menu - where you should be able to tell a shipyard to direct all state ships to rally point X.
(2) [PLAYER NOTES] Each primary object (system, planet or ship) should have the ability to attach a player-editable note. This is extremely helpful in long strategic games such as DW where one game could last several weeks. The best implementation of this concept so far that I have seen is Sword of the Stars.
(3) [EXTERNALIZE ALL DATA FILES] I know this has been covered over in the modding areas, but I cannot stress enough how much longevity and increased popularity externalizing the data into .txt files and allowing modders access gives to a game. IMHO Space Empires IV and V had the best implementation of this so far. In addition, the concept of the modding folder and structure that it uses allows a great deal of flexibility for people to choose different mods.
(4) [SOUND STRUCTURE] Sound is very important to me and is sometimes given the least attention in games even though it forms 50% of the feedback equation along with visual feedback (at least until games that generate smell and tactile feedback become more mainstream). I think DW does an adequate job at sound but I would like to see 3 things that would greatly enhance the sound: (1) as others have mentioned, incorporate both the music and effects subfolders into the customization folder so that we don’t have to mod the original files to change a laser sound effect; (2) when you hopefully externalize the data for the weapons, please make sure to include in the .txt data file the data line for each weapon that references the sound effect so that it can be changed and new ones added; and (3) if multiple weapons utilize the same sound effect I would recommend that they still be given unique names for DW to point to (just copy the sound effect and change the name) - this allows maximum flexibility in the portability and use of several mods simultaneously by allowing sound modders that want to expand on the original sounds and supply unique weapon sounds to simply supply a new set of sounds - rather than forcing the sound modder to also rewrite the data file to force a new unique naming system and thus creating an instant conflict between that mod and any other mod that modifies the weapons data file (for a good implementation of this concept see Space Empires IV and V).
(5) [DECREASE MID-LATE GAME DRAG/DIPLOMACY] I may have missed it, but I do not see an option to force an AI to surrender. If my empire has overwhelming firepower and they are down to 1 or 2 colonies with no hope, there should be an option to force surrender and incorporate them into your empire (for a good implementation of this see Sword of the Stars)
(6) [GROUND COMBAT] I still have Star General on my hard drive, simply due to my love of how that element was incorporated into the game. I don’t think that particular model fits into the DW scale, but I would like to see visual and audio feedback in terms of how battles are progressing (good examples - MOO3, GalCiv 2, etc.).