Down in the deeper depths, you'll start getting metals that offer two additional upgrade paths:
Warp -- lets you warp regions left, right, down or up. Opens things up a lot. The range jump is logarithmic.
Scan -- opens the range for finding a Transmitter. The scan range is also logarithmic and based on the depth so getting warp upgrades is *highly* useful.
The goal is to find and teleport to a Transmitter which is at some deep and far depth. From there you can broadcast and win the game.
Using crystals to unlock new movement capabilities and just research targets in general makes a lot of sense -- this makes the UX a lot better as all you need to know from the outset is how to move and drill and do basic crafting/upgrading, and then the additional mechanics get introduced as you upgrade them.
Similarly, various mechanics in your inventory could be unlocked via crystals like better selection or moving. Macros are a research target. So would Farming and Overflow (and the auto-overflow move thing). Upgradeable drills and Winches would also be a research target.
Research targets should be able to be perused at your leisure with descriptions of what they do. The actual unlock requires some amount of some color of crystal, so moving to other areas makes sense.
Instead of teleports, there should be some way of scanning regions horizontally or up and moving there so you can find what you need and move there. Scans could be upgradeable and show you other region properties like metal distribution or void percentage. The scanning/movement thing would also help with crystal upgrades to drills and winches. Also you could theoretically see what metals upgrade before going there, so you could do a lot of planning tasks in addition to the rest of the game.
Both scans and movement should have upgradeable range and cost metals of any kind, giving them yet another use. They're presumably also gem-based unlocks.
The overall scanning/movement change would tie in waaaaay better with the story and overall goal of the game, which uses that system anyway.
The bottom depth of regions should have pillars rather than a straight line of their solid of choice.
If gems are where feature upgrades are contained behind, then each region should have a fixed number of gems depending on the size -- 1 for 2x2 and 3x3, and I guess scaling up for bigger regions. This makes it more of a metroidvania, you have to actually move around regions to find gems for feature unlocks, which is kinda cool.
Some kind of scanner unlock should tell you where the gems in a region are. Additional upgrades would tell you other valuable things like metal color, metal distribution, solids distribution, voids, etc. Presumably these have an upgradeable range.
You should be able to see an outline of the solids on all four edges of the map in the other chunks. These would be gray and/or gradients but do at least allow you to move around and backtrack better. Alternately, make this yet another feature unlock. Will defintely require some framework changes to implement correctly.
