This is about the geoscape, and my experience in playing a campaign with the svn trunk.
The main thing that interfered with gameplay (other than the bugs) was that when multiple messages appear, only the latest one is shown. There is no indication that there were multiple messages. The consequence of this is that every time I see a new message at the top, I have to check the message history to see if I missed anything. Since most game events are announced with a message (or two, or three...) I was checking that history a lot. Keeping the message history pulled down doesn't really work since it obscures half of the geoscape.
I think this can be improved by adding some flexibility to the number of messages that are displayed at the top. I would want it to show all the 'new' messages when new messages appear, without taking up a lot of screen space in the normal case.
I propose to add a counter that controls how many messages are shown. When new messages appear, the counter goes up by that many messages, so that it will show them all. In addition, once per real-time second it will count down by 1, to a minimum of one message. (There should also be a maximum, so that it doesn't run off the screen.)
The effect is an instant visual indication that multiple messages have arrived, and a short time to read them before they go away and stop bothering the player. If the player didn't read them in time, that's still okay, because the player now knows that they missed a message and can look it up in the message history.