I may be a noob to this game but I've played games since Ultima Online, and play a lot of niche games starbase/wurm online/anarchy online/shadowbane/star citizen/etc over the years.
1. Why not do what eve online does and sell skill packs? They started doing this because without them it encourages people to use alts to bypass the slow skill gains. You could instead be selling skill multipliers that allow us to choose or skill gain pace, and not encourage 5 alt accounts. You could even sell recharge rates for MU as an added bonus.
2. Less skittles is more. A few large rocks per area is preferred, this gives carpel tunnel scanning all these.
3. Resource sinks - you need these for markets to function. There's several ways you can do this -
1. Buybacks - you offer to buy back at a set amount, which allows the market value to remain stable and never go lower than cost to produce, and allows a resource sink for people to sell directly to recycler to get cash quickly.
2. Maintenance - This one tends to be far less favorable by players, but implementing maintenance does have some advantages on the pvp side. Players will have to recruit, and maintain a base instead of just plop it down and pay the fee. They will have to mine resources to maintain the structures.
3. Research - A Tale in the Desert had a unique way of burning resources, it had a community research hub that affected an area in the game so in this game it would affect a 100 hex's and all the neighbors could dump tons of ore into it which then would provide a 5% mining/industry boost (just spitballing here) or more depending on the amount of ore (massive amount) inputed.
4. Casino - I call it the casino, but it's actually really effective and fun way to get rid of resources. Basically let's say there's a ship part - a M wing, and you have a thousand M wing on you. You then could "boost" one M wing with the thousands of M Wings you have to make a +% performance improvement on that one wing. These usually come with some sort of low % chance that the M Wing you burn to improve the other M Wing will succeed.
5. Full PVP destruction - the idea is that the PVP itself is the recycler. Unfortunately there's not anything in the game encouraging fair pvp just griefing - killing solo miners, killing solo freight runners, etc. If the pvp updates turn to be fruitful then PVP could provide a way to reduce resources.
6. Get rid of Mining Units. Having an infinite production of ore will destroy economy