I started to read through the list to avoid duplicating others' suggestions but didn't realize there were so many until I got to the bottom of the first page. Hope this post isn't too boring ...
Only two minor points I'd like to have changed -
When I click on an 'auto-piloting' ship it doesn't remove the autopilot label like in GC1. So when I then right-click on the map to change destination I have to go and see that a new target point has been set. A click should either remove the autopilot label or we should be able to see autopilot routes.
The second point is that launching a transport doesn't seem to increase local approval (because of lower population) like in GC1. This was a great way of maintaining morale while also preparing for invasions, but now I have to build more entertainments ...
Otherwise I really liked the Akilians saying they knew I was building up to invade them, and that if their generals had been 'Intelligent' that they'd've done something about it. As it happens it was the Drengins I took out, but I'd found out who'd be next ...
Great game so far!!