I am a really big fan of games like Minecraft, Stardew Valley, Starbound, and any game that involves gathering and crafting as a driving force of the game.
I have played all of the Yoshi’s Island games and still consider Super Mario World 2: Yoshi’s Island to be my favorite. Other Yoshi games have their charm, so to me, each has its own merit.
I can’t say that I’ve played a game like this before, but Hypnospace Outlaw is the closest and most recent game that I’ve played that I liked that can be compared to this even slightly.
The only game I’ve played that closely resembles this even remotely is FTL: Faster Than Light, as it’s another game that involves managing ship crew and ship systems.