My modest suggestion: you should be able to extract a small amount of Elerium from all those Heavy Plasma clips you end up with. I usually never bother with researching the lesser Plasma weapons, because I know the aliens will abandon them later. This would make it a little bit less painful to manufacture ammo for these weapons.
However, part of the game is that Elerium is supposed to be rare. To avoid unbalancing the resource system, it should be an expensive, inconvenient process, only to be undertaken when absolutely necessary. If it's implemented properly, commanders will consider it a Very Bad Idea in most circumstances. I played around with the ruleset a bit and came up with this:
- Only Heavy Plasma clips will contain enough Elerium to get anything worthwhile. It takes 3 units to make a clip, but you'll only get 1 out.
- After researching the clip, you have to research the extraction process separately.
- It's expensive enough that you can't make Elerium for profit.
- It should take a large amount of workshop space. Like, more than it takes to build a ship. The idea here is that this is a super-dangerous process, so everybody has to clear out of the workshop with the exception of maybe five or ten guys. If someone wanted to tackle the coding, it would be cool if there was a small chance for it to blow up, destroy your workshop, and kill a few engineers.