So to me, the problem with alchemy, and really any type of, collect these items (ingredients, parts, etc) and put them to together to create X is that there is only one layer to it. You go out, eventually gather enough items, and then press a single button and presto you're done. My ideal system would have an added layer of complexity in that once you collect the items, you also then have to go through the process of putting them together, in the correct way. When you're cooking something, there's a lot more importance placed on say, how fine you mix your items, the order you do it in, how well you bake them together. Also, some of the fun is in experimenting with the process, adding in a bit more than what the recipe called for, changing out an ingredient or two, baking it a bit longer for a more crispy crust, etc.
There's already a good system that incorporates stuff like this, aka Cooking Mama. If you haven't played, basically you cook items (obv) but through a process of quick and relatively easy mini games. You're skill at completing these mini-games influences the quality of the final item produced. Something i'd also like to explore, is adding an attribute of Taste onto certain items. Taste is composed of different adjectives (Sweet, Salty, Savory, Crispy, Burnt, etc) that can be geared towards whomever your giving your final product to. While you are completing your mini-games, if it involves one of these items you could intentionally experiment with the rules of the game to achieve a different descriptor. For example, your baking a cake and one game involves measuring out the right level of sugar, going a bit over the "proper" level gives you the end result of a Sweet item. Or if you're cooking a burger, grilling the patty a bit past the proper amount nets you Crispy, but going far over gets you Burnt. I don't think this is a completely original idea, but it would be cool if as an added idea, members of your party have different tastes... and matching your items to those tastes give it a stat boost (extra HP, extra MP, Strength stat goes up for a time, etc).
This doesn't have to be just for cooking, I'm pretty sure the idea of small mini-games and an additional layer of attributes to customize can be applied to any type of item creation system. For example, weapon creation, there was a lesser known game, called Iron Master, that applied the same cooking mama formula to blacksmithing. I know there are some systems out there that allow for certain combinations of items to give a stat boost, and you could add on to that by having certain stock points give a certain "Flavor" to the weapon created... "Flashy, Weighty, Over-Powered", whatever.
So yea, thats what I've got for now, I may come back and adjust / explore the idea further.