Here's my concept for the mining in this game:
At first, I considered what Stardew Valley did- a cave, composed of 'levels' which are each just a room with some resources; the deeper you go the more valuable the resources.
However... I don't know how I would do this, so I came up with a simpler idea that, in my opinion, is just as good.
Randomly around the map are little stones. They give you stone, and oftentimes coal, and less often, iron. You can craft a basic forge with stone and wood, and you can feed it coal and melt iron.
With enough iron, stone, and wood, you can make...
The basic mine! (4x scale)
(It's manual.)
(I don't know how to make it look any more like it's spinning.)
Basically, you place one on dirt, and a hole forms under it. For this basic mine, you click it to mine. Let's say it takes 5 clicks to mine one level. That level is level 1.
Mine deeper, you get more resources, determined by Perlin noise (so some patches may have more than others!). But, the basic mine can only go so deep, say, 20. But you've got more resources. You can craft a better mine now, and go deeper, and perhaps it's automatic.
But with this new mine, there's now a risk factor- the deeper you go, the more chance there is of the mine collapsing and you losing all of the resources stored in it (the manual mine puts the ores directly in your inventory, but maybe the 3rd upgraded mine could be automatic, and have storage) and not being able to mine to the full depth in that area. Well, I'm not so sure about this risk idea, but perhaps I may.
So basically, mines that pull stuff out of the ground to make better mines (and more items).
It would be nice if I was able to somehow make 3-dimensional Perlin noise, but I'll have to be satisfied with a map full of random Perlin noise.