Thanks for the comments folks. I think various users have raised valid points about the potential complexity the extra items will add to the game, as if taken too far it gets overwhelming and starts to feel like bloat (although different players obviously have different thresholds for this sort of thing). However, if carefully curated then additional content is going to make the game more exciting for everyone.
Honestly, most of this stuff is just going to come down to playtesting - what looks great on paper may well fall down because, using the example provided by Ninothree, it might prove really tedious to have a couple of limited quantity rare weapons you have to switch around before every mission for some reason. Or it might not be any more difficult than situations in X1 when you didn't have enough Laser Rifles to go around. We'll only know by testing.
Armour Undersuits:
One idea that occurred to me that might help the situation is to add an additional class of armour - the undersuit / vest. This would work the same as it does in XCOM, where you have an additional "undersuit" armour slot which can contain a variety of different items that provide various defensive bonuses but do not change the art of the soldier (it'd just be another drop-down under the soldier armour dropdown).
This would be cool because it allows us to add a few interesting ideas without messing about with the existing armour progression. For example:
Nanothread Vest (+10 Armour) - 2 Alloys
Medvest (+10HP per turn regeneration, automatically seals bleeding wounds) - requires 4 Sebillian Serum / 4 Sebillian corpses
Nullvest (+50 psionic defence) - requires 4 Psi-Implants / Psyon corpses
Chitin Vest (+25 Armour) - 4 Reaper Chitin / Reaper corpses
etc
None of those ideas are particularly original, but you get the point. Corpses suddenly have a bit more value than just being items to be sold, and after each mission you can craft a couple of additional items (if you want). I guess at that point it's not adding any extra workload to the player, just giving them more items to play with.