2) Expand the research tree. Include additional building/facilities, i.e., harbor, airfield, production center, etc. Currently the research tree is pretty much dedicated to killing things. Would like to see the ability to improve cities more.
3) Along with #2 above, require cities to be connected to the capital in order to use the resource pool. This would help eliminate the problem of factions putting cities in the middle of other factions. As an example. In my latest game, I made the mistake of accepting an alliance. The faction promptly sent a colonizer into my territory and planted a city two hexes away from my capital, but six hexes inside my territory. It has only one hex and is completely surrounded by my territory. This city should not be able to make use of the pool resources and should not be able to expand, yet it does. By forcing cities to tie to the capital in order to use pool resources, it could help stop this practice. Cities could tie to the capital via roads, harbors, airfields, etc. Until tied to the capital they must use their own resources. A one hex city simply could not expand.
4) Upgrading old units. This seems way too expensive. I have found in some instances it is actually cheaper to buy a new unit rather than upgrade an old one. Upgrading should require some cost, but not be prohibitive. You already have the basic unit, you are only upgrading its tools. I would think one half the cost of the upgrades to rebuild the unit. This makes it reasonable and gives you an incentive to upgrade. Currently, it is simply cheaper to build a new unit. No real reason to upgrade.
5) Many have stated this already, but diplomacy is really bad. My last game, a faction offered me a gift. Next turn declared war. Next turn offered me a gift again, and on the next turn offered peace. Two turns later declared war. Next turn offered a gift, etc. This makes no sense. It would seem to me that before offering a gift while at war, a faction would offer to make peace and if refused, then it would offer gifts in order to attempt to gain peace.
6) This could be in an expansion, but I would like to see bigger maps.
7) Research objective Terraforming. What is this for? The tip says it allows formers to improve/worsen ecoregion. What does this mean? I have yet to find a purpose for this research objective.

Overall, the game is becoming better with each version. You guys a doing a terrific job and I look forward to the completed game.