As far as equipping your Troopers go, may I suggest:
- Stack the weapons and other munitions to take only one spot in the equipment screen with a number in the corner or bottom telling how many of that piece of gear are in the base inventory. If a player wants to take one for equipping his Trooper, he just drags the icon to the character's inventory to take one.
- Put in a scrolling bar.
Combining both abilities for the equipment screen would prevent clutter of literally 1 type of item taking up half the total inventory screen. You will also be able to fit more item types in a single screen and minimize the amount of scrolling required.