Having played Galactic Civilizations II: Twilight of the Arnor, I feel that one of the least developed aspects of the game is the logistics associated with star travel. Travel from one star to another is an extremely massive and difficult undertaking that cannot be easily conducted without help. Even with the aid of Alcubierre warp drives, it would take two weeks to move one parsec with the amount of energy (one-tenth of Earth's annual electricity generation) accessible even to one large ship. Larger amounts of energy to create massive warp bubbles are only accessible with the construction of starbases or similarly large constructions with the ability to house thousands of massive fusion plants.
To remedy this situation, ships should only be able to move a very slow speed (say 3 pc/week, maximum) when outside the range of a starbase. When within the range of a starbase (which should range from 0-5 parsecs in all directions from the base, depending on how much the modules have been upgraded), ships should be able to move much faster, technology and appropriate starbase modules permitting. By including this new feature, realism will be added to the game and new diplomatic avenues (such as shutting off access of certain empires to use of your starbases' speed-boosting ability, or taxing the use of your starbases by foreign freighters) can be opened. Furthermore, invasion of empires will be far more difficult, since one would have to lay down and defend a network of starbases in order to move large numbers of ships at any speed.
Another aspect of the game that I did not enjoy was the scale aspect. Planets are almost as close to each other as stars are to each other. Planets should be located in smaller system maps that may be accessed by moving a spaceship onto a star and then zooming in. In addition to being more realistic, the same mechanism could be used to produce a tactical map for fights that occur in deep space (for fights in stellar systems, the system map could be the tactical map as well). Furthermore, the propulsion technology line could be split into two: one (Impulse Drive, Ion Drive, etc.) dealing with intra-system and tactical-map travel, and another (Warp Drive, HyperWarp, etc.) dealing with travel outside a stellar system.