Designing the system for a series of systemic puzzles?

I want to make games that give the player the feeling of being a scientist in another world. That is, the puzzles and systems within the game follow a set of rules that the player needs to discover. Once they’ve discovered the rules, they can then solve the puzzles by deduction. An example of a game that does this well is Outer Wilds.

But I don’t know where to begin when crafting systems like these. An ideal system (in my mind) would be one that feels like a natural part of the world, allows for interesting puzzles, allows players to discover it in layers, but ultimately isn’t so complex that you’d need to earn a degree in it to solve the final puzzles. I think Outer Wilds does this in part by having several reasonably simple systems, and the toughest puzzles are those that involve the interaction of two or more of those. The final puzzle requires you to understand all of the systems fairly well.

For concreteness, the specific game I’m imagining involves a stereotypical magical setting, but that magic follows specific rules that the player will learn over the course of the game. Does anyone have any advise of where to start in creating the rules for such a system, for creating complimentary systems to interact with, or for creating puzzles that reveal just part of the rules? Answers for the more general question posed in the title are also welcome.