So, things I would change, mechanic-wise anyway:
Mutagens - Decent idea, needs a better approach. Personally, I would have loved it if all skills had 1~3 slots and they were balanced (and replaceable) accordingly.
Upgrade Paths - Should have been one massive board with abilities logically linked based on what they enabled you to do in battle. Ex: Quen would be a skill for more physical Witchers.
Potion Drinking - More like the first game. While I understand what they were trying to do, the game seemed poorly built for it. Perhaps a penalty could have been introduced when drinking potions during battle.
Brewing/Crafting - Should exclude quest items.