Great game guys. Having a lot of fun. Here's notes I made after a few large games.
Kept these semi-reasonable, except for the AI comments 
. The ones with * or ** are pretty simple. Hmm, except maybe the Full screen strategic map.
* = Oh PLEASE!
** = Please please!
Civ3 Notes:
- Should not be able to build a starbase if enemy fleet is around (For AI as well) (Area control)
- ** Show movement area when clicked on a ship.
- * Currently cannot counter-offer a surrender.
- ** Remove diplomacy delay please, very frustrating.
- Go to command needs to remember last selection.
- Turn things on and off on the main map, gets confusing on a battle plan
- * OR full screen strategic map!
- * Ship's list should be fleet list. (Option)
- Display ALL move lines for ships, for large co-ordination. (Option)
- * Team sharing of Rally Points or a Ping I guess.
- Planets with long names get cut off.
- Do starbases keep their original resources forever?
- AI players should say out of enemy territory - maybe?
- ** Aliances should be able to share logistics.
- * Hovering over a graph should show the empires name - As the colors are very alike at times.
- AI is pretty good really, but should concentrate on some things. 1) RECON! 2) Area of Control
For example this is my attack strategy:
- Create a line along the enemy boarder of ships
- Move the entire fleet up as to screen, but I move my ships even in to areas without planets, to have area control. (Lots of sensors)
- Take out targets of opportunity... Starbases.
- After that things get messy, but really I focus on controlling sectors of space and creating a front line. By the way the friction level in warfare is pretty good, better than Galciv2.
Thanks.