>>538458015
>>538460440
Like most things, start either bottom up or top down. Most people are usually better at the former.
Simply take a small core you think is interesting, figure out why its actually interesting and what enhances (+) and diminishes (-) it, then lay both of those in a quasi logic-matrix. The overlapping (+)(+) create your logical solutions, the (-)(-) signposts to guide the player the other way, and the (+)(-)/(-)(+) is where you get to be creative in tilting the player one direction or the other.
Meanwhile top down is how most 'puzzles within a non-puzzle game' are done and its usually just asking what mechanics are available, what ways can you restrict the player in something that feels the same yet different, then see if stepping back it makes an interesting picture in terms of play
Personally I think most people are so ingrained to handle esoteric abstracted puzzles that you can almost always go with the former and it'll fit into whatever game you have, provided the difficulty (specifically, the pacing) is on point