What about implementing a failure rate similar to what Morrowind did with Enchanting (I don't remember if they did this with Alchemy or not)? The lower your skill, the less likely you are to create something.
With a low enough skill, the potions could fail. However as implemented in those games, the skill would quickly reach a level where you would have success all the time. What did happen at medium skill levels and alchemy equipment is you could make potions that were so much stronger than in game. At that point, Alchmey became one of the most powerful skills.
I think in Fallout, the potions should be limited to healing items, maybe some posion and flammable/explosives. However potions that increase skills or attributes should be limited in scope if even availible. For sure, make them easilly addictive with bad withdrawls if they are there.