1-Add a hotkey for Rally Points. With GalCiv2 you could click the "T" key and immediately get the dialog to select a Rally Point.
2-Add sorting to ship and planet lists (list on right of screen) as GalCiv2 had. Extra credit if you can also filter ships or planet based on criteria such as ship size or sponsorship of a particular shipyard.
3-Since mining is far more critical to the game, allow the ability for a starbase to have more than one base function (i.e. can be a Mining and a Economic starbase). Of course dual function would have to come at some additional cost.
4- In the ship designer, I really miss having the view tool to set the ship I'm viewing to a particular view (ie.e front, top or side) rather quickly. In building a ship based on a saucer main hull, I lost track of which directions was front/back so I had to save the design to see the ship in the list to know which way was forward.
5-I really miss the Tax Level slider. The ability to raise/lower tax rates in times of war/peace was a nice feature and would not break the new Economy Palette. (I do really like the new palette)