Since there was item limit (and we all hated it...), how about weight limit?
Basic idea:
A transport has a weight limit, and it limits how much equipment you can take on a mission, based on item weight.
Advanced I:
Includes personel and armors.
So e.g. if you really wanna give everyone heavy armor, you might have to do without your dozen spare rockets... Or have to cut back on troop size.
Especially for early transports (e.g. xcf helicopter), you can either have your 6 guys with vests and equipment, or just 4 of them in heavy armor...
This might open up more strategic depth for troop composition and loadout, as you cannot just carry everything you might need anymore and just use on site, or if you do, might have to cut back on team size. Gives a lot of balancing options for heavy weapons and their ammo, as well as tanks.
May keep people (like me...) from putting everyone in the heaviest armor they can find, equip minigun for everyone and keep some spare mags, so may lead to a lot more equipment diversity in loadout.
(very optional extension)
Advanced II:
Includes loot weight too. So you cannot transport all contents of the battleship you just raided back if you did not leave some weight reserve...
May include the possibility of having them transported to your base in a matter of days or so, but some items (stunned enemies etc) would have to be taken by your transport or left on mission site.
(thereĀ“s so much things to do with weight...)
Advanced III:
Missions may have a transport weight limit. For whatever reason... (no idea how to put that story wise. But modders may find a way...)
E.g. special missions limit you to 120 weight, so you can get 4 guys with guns, or 2 with launchers and some spare missiles... even if the transport could hold more.