I'm going to add to this because I was able to play a little more last night.
13a. Feature Request: Indicate how long a trade deal lasts for. Yet another mystery mechanic. You have got to get rid of these mysteries before the game gets to the release candidate stage.
13b. Feature Request: When the agreement expires, indicate what the agreement was, not just that it expired. No, forget that. Instead of offering insulting trade deals every few turns, how about using that opportunity to make a trade offer. You know, a real trade offer, not a "I hope the player isn't paying attention because this is a ripoff" kind of trade offer. If I had open borders with another race, it's fine for that to expire but if relations are still good then we will probably want to renew the agreement (if not expand on it) so let's just get right to the bargaining table.
13c. Feature Request: If the AI is offering a good deal (quite reasonable with a friend), then there should be some indication that this is a take-it-or-leave-it offer OR the player should be able to provide counter-proposals without penalty. I'm Onyx Hive. You can pry my promethion from my cold, dead hands.
13d. Feature Request: In addition to the "I accept" line being more clear and other things to make trading less tedious, how about a second marker on the trade bar to indicate the point where "I accept this as a gift" that would be sufficient tribute to give you a + in diplomacy.
13e. Idea: When a race tells you "Hey your X has been really improving our relations", how about some additional choices: A. Thank you. B. Maybe we could do something to improve relations further (opens trade) C. You know, I've been meaning to tell you, it's time for us to destroy you. No time like the present.
14. Warning: I hit 75% am apparently approaching an Ascension Victory (see 17/18 below) and the entire complexion of the game turned on a dime. Every race turned on me (instant -3 diplomacy plus an automatic dislike that seemed to go beyond that) and this includes races that were declared friends most of the game. Eventually everyone declared war on me. Since I was not focusing on building up my military, the game is probably unwinnable so I am abandoning it. This experience suggests that a diplomatic/pacifist game is untenable, at least for most races. Culture flipping takes too long and there is no obvious counter to the entire galaxy turning on you other than having an overwhelming military. Since the combat system is too opaque at this time, there is no point in attempting it.
14a. Idea: Make the effect of reaching the ascension threshold dependent on the difficulty level so that at lower levels the game helps you win and at higher levels the game makes it harder to win.
15. Intermittent bug: There is a situation where the planet screen draws incorrectly and the left panel gets cut off. I had to save, exit the game, and come back in. Alas, I have no idea how this happened or how to reproduce it. It has only happened once to me. If it happens again then I will take a screen shot.
I have concluded this play-through and will wait until another revision is released to play again.