These observations are from the Milky Way Scenario:
One thing that makes me nuts is the unclear descriptions of what certain things do. For instance:
* Cash an Ideology packet for an improvement. Is it One-per-Player, or One-per-Planet?
* Oboy! Three defensive ships per planet! Wanna know what the maintenance bill will be?
* UP proposal: "Should all wars end?" Did you notice that if it passes there will be no way ever to have war again (something that is actually suggested in the fine print)? Or that it has no effect on war involving minors (something that isn't)? Doesn't seem to stop the minors from begging me to declare war on the Drengin.
* There is nice flyover explanation of the selected ship role once the role is selected. There no hint of the meaning of each ship role in the location where you actually select it.
* A very cool feature: You can select the type of constructor to be built by the shipyards sponsoring a starbase. Unfortunately, your selection reverts to the default as soon as you close the selection dialog, making the feature completely worthless... 
* Get an improvement with a benefit. Is it 10% per planet it's built on, or 10% for the entire civ? Trading Post is a prime example of this. "10% to Trade revenue". Is that:
- 10% globally? (only need to build one)
- 10% globally per TP? (additive) [doubtful]
- 10% to trade originating from the planet?
- 10% to routes passing through the planet's ZoC?
- If so, is it additive?
It makes a HUGE difference. For instance, I originate all my trade routes from my home planet. So I build a Trade Capitol there. Is there any point in ever building a Trading Post anywhere?
* In god mode looking at how AIs manage their worlds:
- Lots and lots of Durantium Refineries. Cool.
- VERY few Culture improvements. NO Tourism or Trade improvements (except the Iridian Free Market thingie).
- The Thalan has about 15 worlds, and has built NO Hyperion Matrix (1PP), his most powerful improvement.
* There are many Pirate bases (shipyards) but the pirates do nothing. When you battle a base, the result is applied to your fleet, but not to the base or its defenders. It just sits there continuing to do nothing.
* There are no Anomalies - at all. So the point of surveyor ships is what?
Otherwise an interesting map that is really taxing my 4GB RAM.