I'd like to see fewer planets, encouraging people to stick around on certain planets longer to more fully exploit them. Better cave generation would help a great deal I think. Terraria had an excellent method of being able to reach incredible depth with only a bit of scaffolding, just a tricky navigation of cave systems.
I can get behind this totally. Right now we are pretty much playing 2001: A space odyssey; The game. You all remember that part where they keep flashing different colored alien landscapes, and at first it is really cool, but after a little while it just gets really boring? That is this exactly. The solution is to make players more invested in a single planet. That way exploring a different one actually feels alien. I would suggest:
1. Remove chests spawning on the surface, or if they do scale the loot so better stuff is deeper. Make players feel like they stand a better chance getting cool stuff from fully exploring a single planet, than quickly exploring many.
2. Remove the fuel system. You already gave a pretty good explanation of why it just forces players to only move forward. I would compensate by making the first quest about fixing your engine so you can jump within your solar system, and the second quest about upgrading it to move between systems, giving players more time to get settled on their initial planet.
3. Make it easier to find shops. Right now people just skim over the highest level planets hoping to find a weapon dealer, and over exposure to all these planets isn't good. I would implement space stations that are populated by most essential NPCs so that you don't have go to searching planets, you can just go there from your ship. They don't have to orbit every planet, or even be in every system, but the ability to just search around for the merchant would actually help I think.
4. Make creatures more varied. Right now every planet has the same set of creatures, just scaled with some numbers and slightly different appearance. I would prefer if only some planets had birds, and only some had bipeds, and so on. Also implement creature specific drops. Right now your tool defines what you get, not the monster itself. Makes everything feel way too samey.
5. Make more work benches. Enough that you don't want them all on your ship because it would be too cluttered! Enough that you want to actually plan out rooms. One for wood work to add crafting recipes for all those wooden items, and one for fleshy items and crystal items. Make us actually need a home base.