Three issue I had when I pulled up the diplomacy screen for the first time and attempted to make a treaty:

http://www.screencast.com/users/Cristofyr/folders/Jing/media/96db57ee-3bd6-4def-86e2-f2130ed5cd76

#1 in Screenshot: Obviously, the text is kind of squished together. And although I click on the to remove that particular part of a deal, it is not clear just by looking at it that it would do that. Placing what each side is offering next to each other with a clear divider between them would help reduce confusion. Make it like how it is on the "Trade" portion of diplomacy. There is a clear dividing line that tells me what each side is bringing to the table as well as what the other side thinks of the deal.

Trade Screen: http://www.screencast.com/users/Cristofyr/folders/Jing/media/6953ca6b-b81b-48c3-bae9-6773467f7cc8

#2 and 3: I find it confusing about who is exactly proposing what to whom. I remember having this problem with Galactic Civ as well. It would be helpful to separate out what I'm saying and what the other leader is saying on other sides of the screen. From the screenshot, it looks like the other leader has contacted me about a treaty, since the buttons on the bottom say "I accept". In fact, I was the one who initiated negotiations. Changing the button to something like "Make offer" would help I think.