Sadly, I did not have the time to read all the posts, but since Mr. Data already told me to put the suggestions in here regardless of potential repetition, here you go:
1. Civilian ships should be retrofittable. Annoying to be endgame and still have freighters with the first engine ever turtling around in the empire.
2. Mining bases should be retrofittable via repair ships.
3. I greatly would appreciate a ground combat research tree, with weapons, armor and equipment, as well as some more detail to the ground combat ( a simple graphical breakdown of what happens on the planet "Master of Orion 2 style" would be enough.
4. On the other hand, planetary invasions should be impossible as long as planetary shields are up. I was able to invade Utopia with 12 troop transports full of Securan Battlechicks(tm) quite early in the game by parking the ships in orbit, and instadropping them on the planet. The ships got shot down in like 2 miliseconds, but hey, I got myself a beautiful planet. Unbalancing.
5. For the love of all that is holy, make something out ofthe victory screen. Like 15 years after I won my first "MoO2"-Game, I can still recite the text of the victory-film... " The power of the ancients is now yours to command... You've crushed all opposition beneath your heel.... yadda yadda". You can't imagine what I felt when I won my first Distant Worlds - in my oppinion better than MoO2 - and saw... that.
6. I Don't know how complex and time consuming it would be, but animations for the races in the politics screen would be awsome. I'm talking about basic stuff, like three basic animations for idling - neutral, angry and pleased, combined with three answer possibilites, approving (nodding or somesuch), disaproving (perhaps growling when angry?) and neutral (shrug?). 9 total animations per race.
Who would not want to see pleased Atuuk? Or angry Atuuk for that matter? Or... pleased Securan? No, I'm getting carried away ;)
7. Technologies to terraform planets to improve their value would also be nice. Not changing their type, just improving their value.
8. And finally, would it be possible to get to pick the racial statistics when I start the game? Alternatively more races, some of which would be able to colonize gas giants?