Honestly, I'd love to see Chucklefish make mining an optional path to follow rather than a gate to better gear/missions. Maybe they could replace pickaxes with mining rigs/vehicles that requires occasional maintenance so they can scrap the idea of pickaxes altogether.
Hmm, maybe later on, a semi-random mission system (based on exploration, collection, or combat) that rewards pixels which you could then use to buy equipment and upgrades, rather than relying solely on crafting them? With the seeded nature of the universe, it should be possible for the quest system to point you to systems with what you're looking for, since the code can figure it out itself, rather than relying procedurally generated locations that exist in a vacuum and disappear when the mission ends. Could maybe also get rid of the extractor or whatever its called (the thing that turns ore into pixels), though on the other hand you'll probably still want to be able to something with old, otherwise useless ores.
(Any upgrades that could be purchased as a result of such missions should also be craftable, but care has to be taken that one path is not supremely easier than the other. Additionally, if any missions offers a specialized tool for whatever purpose, those tools need to make sense as to why they're not player-craftable or accessible outside of missions. No ore-sensing tools that only work when you're on a collect-ore mission, for example.)
In terms of multiplayer, if your target (e.g. a [race] facility on [random] planet) has already been looted by another player who found that place by random chance, you could go back to wherever you got the mission to so they can tell give you another place to try. Or, have AI/ship upgrades that let you ping planets/systems/the galaxy map (possibly with varying degrees of accuracy) for the kind of location you're looking for (e.g. a specific race facility, pirate airship, etc). In the worse case, you could perhaps overlay standard blocks with the quest-related items you're looking for, such that they're only visible while you're on the specific mission.
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As an aside, I also like the idea of scrapping pickaxes altogether and instead having those be suits/mechs/machines/vehicles that require upkeep/maintenance. Just to help explain why the matter manipulator is inferior, even at 0 upgrades, to a blunt instrument. (Though I guess that's never really going to make sense anyway. Why not just have a mech with dual/quad/n matter manipulators?)