There should be a way to unload unused items for craft equipment. I've got all this stuff...
...And this much goes unused. The way I equip my troopers before combat is that I equip EVERYTHiNG on the skyranger, then I distribute it to my troopers, then I take away everything unused one by one. Slowly and painfully. Take away exactly 13 grenades from the skyranger, take away exactly 8 stun rods, take away exactly 4 laser rifles, etc. No unused gear lying inside the Skyranger when the battle starts, but I had to do that manually.
If I try to reduce how much "taking away unused items manually" I do by taking what I think I need, that doesn't work either, because I'm terrible at predicting how much they'll actually need, and usually take too much or too little. If I just take everything on the skyranger and leave all the excess gear on the floor, then I'd get screwed over if I were to play UFO Redux/Area 51 (Because it has missions where your objective is to escape, and all that excess gear is left behind). Currently playing mostly-vanilla XCOM, then I'm trying the Area 51 mod again.