In these past months, I was really looking forward to the game's alchemic system, to see what they could come up with. Why the change? It sounded great from the tidbits of information we had gathered. So, the following is how I thought alchemy could have been like, based on what we knew and what I think can solve the apparent issues that required auto-refilling potions. As always, this is to be intended as nothing else than constructive criticism pointing at what I, in my humble opinion, honestly believe would make the game better. Needless to say I'm also rooting these ideas in this thread's feedback, and mostly in the first game's system.
First of all, no auto-refill. Sorry, but that's just a bad thing for me.
"Meditation" and "support" potions: the most powerful potions are to be consumed during meditation, the weaker "support" ones anytime. "Meditation" potions have a higher toxicity, and their effects are more powerful and last longer than those of a "support" potion. Alternatively, "meditation" potions can also be at the same level of "support" ones but their effects can be activated on command.
You have a limited amount of "support" potions you can carry and thus use in a single battle (say, three in total, such as one Swallow, one Golden Oriole and one Tawny Owl) and you always have to keep an eye on toxicity levels. You also can't have too many potions in your inventory at a time, and meditating for one hour resets all your potion effects and toxicity.
There still is a spot for "mutagenic" potions (you drink them during meditation and their effects, as well as their toxicity, last forever until you deactivate them), but I'm not really keen on this idea. Toxicity levels could become really hard to keep track of, and I liked the concept of rare monster ingredients which unlocked unique abilities; this could also add to customization and replay value.
Upgrading potions: Not a bad idea, but I believe this should be relegated to rare formulas instead of rare ingredients, perhaps found in those "witcher hideouts" of the monster slayers of old. Rare ingredients could be used for mutagenic potions as in the first game (as indicated above) or to enhance a regular potion, but this could lead to frustration in the case of it going to waste.
Plentiful ingredients: every plant gives, for example, five ingredients; they don't have only one flower or leaf, after all. This way you can make several concoctions before being worried about running out of stock, and you won't need to chase every last celandine you spot in the corner of the map. There would be a dedicated and limited space in the inventory for them (say, thirty ingredients per primary substance), and if you really hate wandering the wilds for ingredients, you could stock up on everything you need at a herbalist's (who would NOT sell witcher potions, obviously, but you can sit by their fire and make them yourself).
Additional substances: also known as Albedo, Nigredo and Rubedo, which confer secondary effects to the potions you prepare. Possibly limited to only one between "meditation" and "support" potions, but not necessarily.
Alchemical bases: alcohol and the White Gull potion as a base, with varying degrees of quality. In the first game quality dictated the number of ingredient slots for a potion, so that you could only make the best potions with high-quality bases; this could be modified or expanded upon with adding positive or negative side effects, modified duration, basic power of the potion, and so on. Alcoholic bases would have their separate slot in the inventory as well, and you should be able to use a single bottle several times (also not to make Geralt carry ten bottles of vodka in his bag).
Bombs and oils: Mostly identical to the first game's system. Black powder and grease as bases, not sure about additional substances but there could be creative uses for them.
Can't think of anything else at the moment, and I just wrote what came off the top of my head. Feel free to add your thoughts and ideas. As far as I'm concerned, I believe alchemy should reward foresight and carefulness, yet not discouraging experimentation and audacity. I think this system, while maybe not perfect, would be great at achieving just that.