When Terraria was out, everybody had four or five tools -- hammer, axe and pick come immediately to mind, and there's probably at least one or two I'm forgetting -- and each had its own hotbar slot. On one hand, this made it possible to selectively upgrade ability to dig/mine/cut based on personal preference, but on the other hand, it meant that four or five tools appeared on the hotbar at any time. That really reduced players' flexibility as far as item use, because at most times the first four or five hotbar slots -- the most accessible ones -- were occupied by tools and weapons. Most players either had to place their tools in an inconvenient part of the hotbar (keys six through nine) or place their items in one, which was inconvenient. Here's the deal: like in Terraria, most blocks in Starbound have about one valid interaction type. You probably want to axe a tree rather than mining it, and mine rock rather than axing it. So, in most cases, there's only one way to really interact with a block -- the choice of which tool to use is not only a false choice, but it's a false choice that takes up four or five hotbar slots when it shouldn't need to take any (or at least any more than one). The solution to this is to expand the matter manipulator -- the game's basic, initial 'manipulate block' tool -- so that all block interactions can be handled with it, even post-tools. The development team should include upgrade slots for the matter manipulator that fit each tool type, so that you can still use the matter manipulator as a single button, but it scales based on the tools you have access to, and as a result, you have all the hotbar space you would otherwise lose. Instead of making a pick and using it, you would make a pick and slot it into the matter manipulator's 'pick' slot, after which it would take on that pick's rate.
I deeply agree with this proposal. Instead of "copper pickaxe" just write "ores manipulation lvl 1" and upgrade the speed of the matter manipulator according.
This would be wonderful, although I think it could potentially be a bit less easy to do, considering the Matter Manipulator has significantly better range than picks and axes. To keep it balanced, maybe instead of slotting in a pick, there could instead be a way to make upgrade chips for the Matter Manipulator, that would be a bit harder to obtain but significantly more effective than a pick by itself. It would add a better sense of progression, going from using a short-ranged but effective pick to later on upgrading your Manipulator into a world-destroying juggernaut.
I didn't respond immediately because I didn't have a precise thought, but I've got the germ of an idea. If the developers could somehow distinguish the role of picks from the role of matter manipulators (perhaps picks break a larger area of blocks as they do now, but at much shorter range than the matter manipulator -- like in your suggestion), they could make the manipulator upgrade require a pick as a reagent. What I mean is that if they made it desirable to have both a pick and a matter manipulator at the same time that would make it so that the matter manipulator is always as good as the previous pick tier but not as good as the tier you're on (unless you make two). That could still lead to tool hell in the case that people just decide that there's no point in making the manipulator upgrade, but I'm thinking that if you distinguished picks into a more niche application by further limiting their range, it might still work out. It's not an idea I'm too comfortable with and it's certainly not the primary thrust of my suggestion, but I think it might be worth considering.