Sprite food has essentially destroyed the purpose of Moonstone (blue) and Valestone (green) due to their new role as "useless" compared to the other three that are now exclusively used for the aforementioned purpose. Further, mineral collection is boring. I'd like to propose some changes.

•Revamp pet food with Shard materials.
The mineral system was killed with the addition of sprites, as their role in changing the Arcade gates was diminished. Instead of deleting a highly useful and community-driven team effort, it would make more sense to use Shards, the 0* materials everybody has too much of. Charging, say, 50 red shards for a Power Star would offset the rarity problem, and it would free up the actual minerals for independent use.

•Make minerals drop Shards when broken.
This is a no-brainer. You crack a rock open, you get the gemstone in the middle and rubble on the side. The smaller the Deposit, the larger the shard drop (Shiny=1, Large=2, Medium=3, Small=4). It's the good ol refinement process.

•Get rid of "mineral rooms" and make rarer, interesting ones.
There is absolutely no reason Minerals can't appear anywhere else in the Clockworks except for these square storage rooms. I'm in favor of getting rid of those, making mineral drops an uncommon appearance in any room, and making rare scenario rooms that are organized mineral storage rooms (shelves, robot arms, gremlin knockers, something that shows how all these rocks get in one room artificially) full of minerals that drop larger deposits based on your depth.

•Reinstate the Arcade mineral system.
With the pet food out of the equation, everything is back to normal.

I really think this would declutter the system.