I prefer DFs UI as it is now with some tweaking and a face lift. And I won't say this often, but I think that DF should look to M$ apps for UI design. Here are my ideas that may or may not have been shamelessly lifted from one of the afore mentioned apps:
No open windows, all windows slid closed, action window takes full precedence
As the mouse hovers over a small tab, the window expands (exposes clickable selectables as well as hotkeys)
Messages would be on the bottom separate, it would be expandable and shrinkable to whatever height is desired or hideable altogether, then also some kind of dropdown which separates the kinds of messages.
The stockpile menu can be tacked so it stays open and then the messages could be opened along bottom of it.
or the stockpile menu could be floating alongside the main window if desired so it would always be visible or could be put on a separate monitor.
In summary, pretty close to what Jiri's got laid out with everything being hideable. I think i like the right click idea, but I would have to see it in practice to know for sure.
Edit: The Action Window wouldn't squish and stretch like that, that is just me being a little lazy and I'm at work...
The mockups are good for workflow and overview. There is only two problems with them: (1) they will hide information and require you to open and close panels which can be argued to slow down interaction (but is a minor problem); and (2) they are very much in the style of applications, not games. This Visual Studio-ish interface will probably detract from the immersive experience, even if it is good UI design.
I personally prefer the original mock-ups in this thread.