Got a bit more to add now:
ESC should clear all open windows. 1 press to clear them, a 2nd press to open the menu.
The science clipboard, when open, gets in the way of pilot portraits. There doesn't seem to be a way to close it, except for the button in the app bar. The above would be a good fix but better to make it a movable window, like all the other pop ups.
The compass on top of the navball tends to go all over the place when youre looking at poles, sitting on the pad, etc. Y'all might consider adding/expanding the deadzone for that to keep the compass under control. This could also help with strange SAS behavior.