Let's have a look at resources you can get in the game.
First, by how they are used:
- Supplies: you spend them on maintaining ships and repairing them (constant use), surveying planets, building space infrastructure and settling planets. Can be simplified to "you need it to do anything".
- Fuel: you use it for traveling in hyperspace and for emergency burns (nearly constant use), and also for bombarding colonies. Can be simplified to "you need it to go anywhere", which you need to do for most things.
- Crew: required to maintain your maximum CR and lost when ships are damaged. Almost always required, but in a boring way.
- Marines: used for raids.
- Heavy Machinery: required for salvaging and surveying, used for salvaging, settling planets and building space infrastructure. Not as necessary as previous three, but you still always want it, unless, for some reason, you are not interested in salvaging (free loot!).
- Metals: used for building space infrastructure.
- Transplutonics: used for building space infrastructure.
- Volatiles: used to run neutrino scanner, which means that it's vendor trash in some runs.
- Food: vendor trash.
- Domestic Goods: vendor trash.
- Luxury Goods: vendor trash.
- Drugs: vendor trash.
- Harvested Organs: vendor trash.
- Heavy Armaments: vendor trash.
- Ore: vendor trash.
- Organics: vendor trash.
- Transplutonic Ore: vendor trash.
- Volturnian Lobsters: vendor trash.
Right here we can see that many commodities are useless to the player and that supplies and fuel are mutually redundant, metals and transplutonics do things that supplies do already and that crew is almost entirely redundant after ship acquisition. Not good.
However, perhaps those similarly used goods differ in the way the player can obtain them reliably?
Notes: by "colonies" I mean "for sale on colony markets", "after-battle loot from trade fleets" and "player-owned colony resource stockpile". I just don't want to write all of that every time. "Exploration (in small quantities)" relies on dismantling randomly generated space infrastructure. "exploration to some degree" means it's not exactly guaranteed to be always gained, but it's still frequent.
- Supplies: colonies, after-combat salvage, exploration.
- Fuel: colonies, after-combat salvage, exploration.
- Crew: colonies, exploration to some degree.
- Marines: colonies.
- Heavy Machinery: colonies, after-combat salvage, exploration.
- Metals: colonies, after-combat salvage, exploration.
- Transplutonics: colonies, exploration (in small quantities). I am not sure if it can be gained from usual after-battle loot or not, I don't remember it right now.
- Volatiles: colonies, exploration (in small quantities).
- Food: colonies, exploration to some degree.
- Domestic Goods: colonies.
- Luxury Goods: colonies.
- Drugs: colonies. Different in that you have to smuggle it in most places.
- Harvested Organs: colonies. Different in that you have to smuggle it in most places.
- Heavy Armaments: colonies.
- Ore: colonies, exploration to some degree.
- Organics: colonies, exploration to some degree.
- Transplutonic Ore: colonies, exploration to some degree.
- Volturnian lobster: a unique colony.
There are only three categories of resources here: those you get from everything, those you gain from colonies and exploration, and those you can gain reliably only through colonies. The most boring way is also the most common and reliable.
I just can't help but ask why? Why are there so many resources, if most of them can be gained in the same way, are used in the same way and you are hardly ever forced to choose one resource over the other.
If I were to remove everything but supplies, there would be only few gameplay changes and none of them would be ground-shattering: tankers and liners would be pure lore ships (which doesn't hurt, since they just aren't very interesting in the first place), Safety Procedures 3 and Navigation 2 would lose a little impact (since there's no fuel anymore) and, finally, after a bad fight you aren't crippled until you go to some colony and buy more crew.
While it's intuitive to most people that there would be several resources in the game, I just can't help but notice that most are too similar to one another not to be redundant and their presence just doesn't bring much to the game. You can take the easy route and remove redundant resources, do it the hard way and improve resources so that they are gained in different ways, spent on different things and giving different gameplay challenges, or do the lazy thing and just leave it as it is. Either way, I need to think more about the best thing to do, and you most certainly need to think even more.
Edit: during a brief walk with a dog I've realised I've made a slight mishap and forgot what I was writing in the middle of it. I meant to list only reliable ways of gaining resources, not all of them.