Okay. Naming that "crystal" was the worst idea ever.
Probably
Well, then I took the time to revamp this proposal. Here's the new version. Forget everything I said before.
If this option is enabled in the game's options (this is not a plot nor a MF), a new resource is added to the game: Ultranium.
It's displayed beside metal in light purple; it have its own, separated maximum reserve; each structure providing resource storage also provides 1/5 additional storage dedicated for Ultranium. Salvage is also tracked and gathered separately.
At galaxy's generation, 1/5 planets are randomly picked (not human homeworlds) and all their metal deposit are replaced with the same amount of Ultranium asteroids. When captured by humans, these asteroids can be mined by regular metal harvesters. All bonuses to metal harvesting apply to Ultranium. OCStations on Ultranium planets gives ultranium instead of metal (building economical OCStations on such planets might be an interesting choice).
A new economical device is available: the Ultranium converter. It converts Ultranium into the same amount of metal at a fixed rate for a small amount of energy. Several may be built to increase the conversion rate. Converting metal to Ultranium is not possible.
Some ship types, preliminarily tagged "Ultranium Eligible", have their metal price replaced with an Ultranium price, with the same amount. These ships consume Ultranium instead of metal when built. When destroyed on human-controlled planets, their scrap is added to the Ultranium count. The AI doesn't track metal/Ultranium type for its reprisal mechanism.
Proposal: Ultranium-tagged ships are the ones in "complex" available ships option but not in "normal". That makes 22 out of 72, not counting the base starships. (I would personally add the attractor drone and the youngling nanoswarm and remove the youngling vulture and zenith medic frigate, but it would be only marginal changes.)
Each ARS has at least one metal and one ultranium design. The three designs are shuffled to let the first (obtained without hacking) random.