This unit upgrade option is long overdue. We the people say YAAAAY!
Anyways, to streamline the suggestion above, treat each upgrade as a 'check box', instead of an 'execute' box, and then add an 'apply selected upgrades' box to the bottom. You could have an 'upgrade all' box next to the 'apply selected upgrades' box as well.
Also, a 'drop down menu' to the left of the check box, showing all available upgrades might be nice, so if for some reason you wanted to upgrade to a lesser weapon or armor to conserve gildar, resources, or whatever, you could do a lesser upgrade. Or choose those initiative boots instead of the armored boots as mentioned above.
This would get tricky with special items (rings, amulets, etc.). I'm thinking, to keep things simple, you only be allowed a single item upgrade at a time (choose one from the dropdown menu). Yes, if you wanted multiple items this would take longer/multiple rounds with the upgrade window, but the alternative is to give each item it's own line, which might clutter up the upgrade window a bit much in the later stages of the game.
So, the buttons at the bottom might be:
[Exit Window] [Apply Selected Upgrades] [Apply All Upgrades]