I understand why they are made, I do simply not approve.I'm not saying that you have to like it. What you choose to like is your own prerogative, I'm simply offering a viewpoint to why these changes are being made. I'm a hardcore RPG fan as well, but I'm ok with elements being "streamlined" if it makes the gameplay more compelling.
The fact is all other elements and every impact this change has has to be considered.
And my conclusion is that while the auto-refill might cater to the enjoyment of some people and convince some people to try alchemy it will also ruin the enjoyment for a lot of other people who grew to love it.
Simple solution: establish other OPTIONAL systems that allow an EASY access to low- and mid-level potions for people who do not WANT to bother with brewing them.
Still, even if those changes are done there is NO guarantee that the potions will be more "balanced" in their effects as you are hoping.