Let's assume you don't actually mind using your keyboard:

F6 will lock the GUI on top.
Hit it again and the GUI will be unlocked (and won't appear even on mouseover) so you may enjoy more of the carnage.
Hit F5 and F7 to toggle radar map and unit cards respectively.

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Resolution does not change? You might benefit from checking the -ne switch; also keep in mind that the GUI of RTW was optimised (by CA) to be rendered at 1024*768.

1200*900 is considerably larger; hence the blurry look of particularly portraits. You're lucky your monitor actually comes in this 4:3 aspect ratio: at least circles are actual circles.