I just realized not long ago that you can drop potions and destroy them. So for role playing sake, what I am going to do from now on is once I meditate, I am going to trash all potions/oils/bombs except a select few of each type. If I need a specific one that I don't currently have, I will "prepare" as witchers do and go through the process again. This will also help in what is bothering you. It bothered me too. Way too cluttered.
80% of them set in my inventory and never get used.
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It would be nice if we could select which potions get refreshed.