You know, I was thinking about this thread, and the original suggestion of being able to clear the Sky-Ranger of excess inventory items isn't a bad one.
If someone wants to load up all his soldiers with as many grenades and flares as they can, the easiest way is to throw more into the Sky-Ranger than you need, go to the inventory and allocate them to your soldiers, and .. there's no easy way to throw the un-allocated ones back, right? If you mis-count when putting the assorted stuff back individually, you start taking things out of your soldiers pockets, and that's never good.
How about something like this: A fake item at the bottom of the list you're transferring to the Sky-Ranger/Avenger called "Remove Excess Items" (see image), which just takes things that would be on the Sky-Rangers floor, and puts them back. Then you can better keep track of what stocks you have, and share the truly precious spares around your other bases as appropriate.