Since we haven't seen the flags yet, I thought i'd make the same suggestion concerning them as I did concerning the troops. Should be much easier to implement with flags. That would be to have different size options for the flags. Scale and over scale for folks like me that can't identify who is who by uniform alone sometimes. lol
On a different note, I've been looking at the LGA manual printer version.pdf from LGAA 1.3 and thinking of getting it printed out. Seems like it made very bad use of space being turned on its side and having the exact same header graphic on every page. 76 pages when it could have been more like 40 or so. I think this is VERY IMMPORTANT because if people are going to play your game(the whole point of making a game) its going to be very important that they print out a manual. Also, the demonstration graphics that where included are fine when viewed at 150% or so in Acrobat, but if they were on a printed page they wouldn't be useable. Even if you plan to include a printed manual I think these comments are relevant as you'll save money on the printing and have a better manual.
Cheers!