The menus, by far, have to be the worst culprit. While they are functional, they can also be hard to read. For the main menu. Some sort of translucent image, even just a simple rectangle, behind words in the menus would greatly increase readability.
Next, the console. It works well, but now it just needs some sort of organization. I don't mind that game messages, server messages, and player messages are all mixed into one area because people aren't very chatty in game anyway. However, if you take a look at the console in a game like UT3, you will see that it has a background to it. Just a simple black background with a coloured outline. It needs to be compressed somewhat. It looks fine on my Windows desktop with a 22" 1680xiforget display, but on my 1366x768 Linux laptop, it clutters the screen a fair bit. Compressing the messages at the top of the screen would do wonders at lower resolutions.
As for the rest of the in-game HUD, Here is a very... very dirty mockup I threw together in inkscape.

Please bear in mind, I am a programmer, not an artist! But I hope you get the general idea. You have all your info in one place and there is considerably less clutter. It tells you more with less. As for the console at the top, it would only appear when text is being input. It would not be there otherwise.
All of these things could also be customized like the cycles are. IE: Different colours and transparency values.
I am willing to help with the HUD. I have a 2D drawing engine made up that, if it was coupled with whatever font engine Arma uses, could make implementing these things easier. I also was talking with people in the IRC and someone was saying that proper shader management was needed. My engine also offers a decent shader manager that I believe could work well for your purposes.
I am looking over the Arma source code, but if there are things the developers wish to point out to me, please, let me know. However, I write all this while I am very pressed for time. I have a multitude of other things to do for my studies, and those currently take priority.