I know we already have a lot of these, but I don't see any recent threads on this and I think mine might be unique, so please hear me out.
First off, we're obviously going to need 2 new battle sprites in order to prevent an excess of Valestone and Moonstone in the system. Based on the recipes Green Shards and Blue Shards are used in, the Valestone battle sprite should probably be Freeze and possibly piercing themed (perhaps using an icicle attack similar to the Jelly Cube's thorn attack); and the Moonstone battle sprite should be Shock and/or the most balanced sprite, a decent choice in any Stratum, similar to the Leviathan Blade (increasing speed as an ability comes to mind, useful both defensively and offensively, and also being useful for end-game speed runners).
Second, after the Valestone and Moonstone market has had time to settle, gate building would be re-implemented, but slightly different: instead of consuming the minerals entirely, they would be "depleted", returning the same mineral type but depleted. Note that the description for the Shard Bomb confirms that at least Crimsonite can be depleted like uranium, which also implies that it can be used as an energy source (for gate building). The recipes for sprite food would also be modified to use depleted minerals instead of the charged versions. This way, minerals could still be used for both gate building and sprite food, without impeding each other.
Actually, you know the gate in the Lab that's blocked off?
Maybe use that idea, but use the gate in the lab and have it so that it doesn't affect the arcade at all (too many people already have Drakon, Seraphynx and Maskeraith). You could, if you really wanted to, implement a system where you drop off the minerals in the Lab, and over the course of a day up to 100 minerals are depleted. You can come back at any time to pick up your crowns (probably less, like ~5 per mineral) and the depleted minerals.
Side note: since you'd presumably still need charged minerals for the Geological Survey (or whatever they're called) Prestige missions, you could have a "recharging" station where you could charge your minerals. I'd say you could use Fire Crystals to do that: Cracked is 1 mineral, Dim is 3, Warm 5, Glowing 10, Shining 25 and Radiant 100. The Radiants spike up so much because they're so rare compared to the other ones.