Wow, there's a lot of reading here, and many, many great ideas. Many of my comments are seconds of others' ideas, but I'd like to bring them up, as well as some of my own:
+ A previous/next button on the main display, with a pull-down menu for ships, suns, spacestations, etc. that would allow me to highlight the previous or next item on the big screen without having to dive into sub-screens or re-zoom the big screen.
+ Arrow keys move the main map, and have diagonal movement.
+ A "What will you give me for this item?" option in the trade screen, as in Civ.
+ Random opponents button in the sandbox game.
+ Ability to rename stars, starbases, etc.
+ Sound cues for events like war, peace, and button clicks.
+ Ability to mass-delete ship designs from previous games.
+ Show the value of tech being traded, so that rookie players like myself don't end up trading Ultimate Weapon Tech I for a Pile Of Dry Sticks I. Civ IV does this.
+ Clarify the minimap to get rid of the "glare" at the top.
+ Make upgrading your ships easier, to allow for the removal and replacement of parts.
+ An "Undo Last" button on the ship creator screen, or even better, progressive Undo's, as in Photoshop.
Thanks for hearing me out!