Digging is a fun part of the game, but I think you get that upgrade too soon. If it were me I'd leave it in, but work it into a later upgrade of some sort. I don't mind the rocks, that was kind of a new thing I'd not seen done in this type of explorer game. You always see double jump and jetpacks, and keys or ammo types that unlock doors, this was original as a barrier that caused you to need to dig tunnels to find ways around them. Maybe there could be a pick upgrade at a later stage to break the rocks too.
I'm not familiar with any of those tools you mentioned, I've used gamemaker and Unity myself.