I think this sentence really captures something that could be fun. You're hitting on a potential metroidvania idea here.
For instance, you want to make a potion that helps you see in the dark but before you can do this you have to get a certain ingredient then ground the ingredient with a mortar and pestle.
Say, for example, to earn the "next ingredient" you need to go through a dark area of the dungeon, then you figure out you need to stack up on ingredients to make a potion to see in the dark.
But then you see that a part of the dungeon has collapsed underwater, so you know you need a water-breathing potion, which puts you off-course searching for the components to make that potion.
It would be an interaction between a longer-term goal, broken down into obstacles which in turn lead you back to reading your manual and uncovering information (what ingredients, how to use them, where to find them) and immediate goals (finding the ingredients in the dungeon).
I think such a game would be appealing, especially if you challenge the player once in a while. They see the obvious dark, thus they'll make the easy assumption that they need a dark vision potion (which is ok) or they could've done their job of studying the manual and uncover a pass-through-wall potion or flying potion that allows them to simply avoid this obstacle in a clever and simpler way. You could find hidden areas using more complex potions that aren't necessarily required for the basic walkthrough, but it could expand on finding rare ingredients and make even more impressive potions.
That said, that would shift the focus of the game towards completing the walkthrough rather than making more potions and this could sidetrack you from your objective.
Interesting thought, I like the idea that the environment can be as much as an obstacle as the creatures inhabiting it. In this kind of sense the player would have to either stack up random ingredients or make lots of back and forth journeys to get the right potions to complete these obstacles. I don't know if this would be challenging or tedious though. I'm going to try and keep the walkthrough to a basic level so the player feels free pretty much do whatever he or she likes.
I'm not sure that linear things like quests would work in this kind of game but it's one of these things that I'm going to think about. I'm also not sure how one would beat the game or reach a final objective. Maybe it would be to create all possible potions but that would be suggesting that there would be a finite number of them. I like the idea of have millions of combinations of ingredients that combine certain effects but I also like the idea of having pre-determined potions because they would all be unique. I think that I would probably go for the more unique potions and have a finite amount of them because it would make brewing them more interesting. "Oh you put a little too much of this so now the whole potion is ruined!".
I don't the idea of the game telling you that you have ruined a potion. I would rather the player find out the hard way in the middle of a danger zone ;)