Don't know if EDCE is still under development, I suspect not but if so ...
One annoyance is units onboard ships prompting for orders if they happen to pass through a city, passing through should mean passing through. This is also annoying for units on board air transports which have landed for refuelling but I see no easy way round this.
It would be nice to have a whole map view with the current area indicated, perhaps toggled by a button?
Sea bees can travel on land so should be shown in land production dialogs.
Will add more as I think of them.