I read through all the suggestions so far, and have a few to add.
First the ones already covered:
* Add a checkbox to prevent deficit spending - I get a lot of income from trade, and when it drops off I can run -$$$ for many turns before I notice it.
* Leave trade details on the board if the offer is refused.
* Show % completed for projects that have been left idle. When I view a planet and want to check other build options I want to be able to go back to what I was working on originally.
New:
* Bug? When I try move a ship onto my planet, and there is a trade vessel there (the small one for ongoing trade) I can't do it (am asked to attack the ship).
* Some way to see what is causing morale problems on a planet.
* Targetted destabalisation spending. Sometimes I'd like to just focus on trying to get a system in 'my' sector to switch to me. I don't care about the enemy as a whole but just want to focus spending there.
* When choosing amount of influence or money in a trade session, there should be a cancel button so that you can quickly exit without applying it to trade.
* Add an option to not load the cut scene at the start of the game. I've seen it once, don't want to see it every game that I play
* Make government descriptions provide more info. The republic description just says that colonies have more control over projects, but doesn't tell me what that means in gameplay (chance of rebellion, better production, senate).