Go into the game options and find the GUI menu(i think) somewhere there you can change the colours and size of icons. change the enemy icons to a darker shade of red and if you like set to size 12, to lose the 'neon' feel. Thats just a personal pref.
Here is the trick for your SA, turn the friendly icons to the same blue as the sky. This way friendlies above you will show up faintly against cloud or just be a dot. All you will see is the red guys above you. Looking down you will see friendlies against the darker land. If you ever need to ID a friendly above you just check the radio list or send them a check six and watch the text buffer.
Try it, see what you think. I suspect you could find yourself being hit by an unseen high enemy alot less.
S!