Intelligibility: Don't make the player memorize recipes off of GameFAQs to make the potions they want. Instead, let them learn The properties of different reagents and processes, so they can think their way through making a potion, then tinker with the method to tweak performance in a more opaque way.
Physical vs. Chemical changes: Let the interaction of the ingredients yield a "flavor" of effect, and then the preparation of the end product determine the nature of the effect. A fire potion is a simple recipe, but the same ingredients can be mixed in different concentrations to get a different effect. A heavily diluted potion could be drinkable and raise your body temperature, a lightly diluted potion could be a molotov cocktail, a concentrated potion would be ore like napalm and a totally dry mix would work like gunpowder. Same works for other effects, and mixtures that have more than one property. So I could make a flask of goop that contains dry fire and wet poison and it explodes on contact and spatters the area with venom, or I make a mix of thin fire and dry health that'll immediately cure status ailments and give me a five-minute resistance to cold environments.
Equipment requirements: What should require a lab, and what can be whipped up in the field? What role should character skill play in the success or failure of an experiment? Is it practical to carry around a bunch of test tubes with you?
Player skill and time-critical processes: Maybe some tasks would have a fun little minigame for how long to leave it on the heat or how vigorously to stir it or whatever, and there would be a "sweet spot", akin to swing strength in a golf game, so you can whip up a decent mix fairly easily, or you can try to paint the line and run the risk of burnign it or blowing it up or otherwise wasting your reagents and hurting the end product.
Risk and precautions: I saw a documentary about early 20th-century chemists working with extreme low temperatures, and the glass equipment would routinely shatter. Half the researchers in the group photo had eye patches on. Take off your +4 Helm of Telepathy and put on your +2 Goggles of Lab Safety, man.