Aside from all the story/narrative issues the game has, it also has a bunch of technical/design ones, alchemy/meditation and itemisation/loot are definitely the greatest offenders in my eyes.
I got a few suggestions to how loot and itemisation should be handled, that in my eyes would have made the game more enjojable and imersive, also more lore friendly and consistent:
*Merchants and blacksmiths should only require special ingredients from the player(like meteorite ore, griffin feathers, gargoyle skin, etc) when asked to craft something, not materials/ingredients such as: lumber, iron, ropes, etc, they should already own and provide that kind of materials. This is one of the things i hated about The Witcher 2 and sadly it made a comeback in The Witcher 3.
*Less "junk/trash" items please. Why would Geralt go around picking up rusty swords, chandeliers, dolls, etc etc... It just saturates the world with unnecessary stuff and crowds the inventory. It also breaks the immersion. Their placement should also be more hand-placed and less random.
*Lesser amount of Armors and Weapons available overall, but with more meaningful customization and upgrades instead(a wider variety than in The Witcher 1, but with an upgrade system similar to that of The Witcher 2, however with some visual changes added when the item is upgraded(like in "Mars: War Logs", or "Bound By Flame")
*Fewer amount of blueprints/diagrams; why would Geralt be interested on knowing how to build a simple Temerian sword? or a commun Redanian Armour, etc? Keep only blueprints for decorums, bombs, potions, oils, Witcher Gear and Epic/Legendary/Unique gear.
*Tooltips and information regarding the background of specific items. It was very nice on The Witcher 1 reading the small info that came with certain objects and special weapons, it added a lot to the inmersion and created greater emotional attachment to our gear.
*Geralt should already start the game with all basic diagrams for basic potions, bombs and oils. He no longer has amnesia, so this knowledge should not be something new to him. He should only have to find upgrade diagrams for those, as well as the diagrams for the basic decorums(as they are new to The Witcher games).
*Remove Equipment Level Restrictions, if we managed to fight a level 20 monster guarding the treasure while we were only level 4, then we more than deserve to be able to use the level 20 sword that we looted...
*Re-balanced economy(how is it that if a whole village has to poll money for a contract, and all they can afford to pay us is 200-300max, then how can a single water bottle cost 20+ at an inn, or a simple sword 800?
*Buy Back System for merchants and blacksmiths. Sometimes we simply click on the wrong stuff and end up selling it, we should not be so harsh punished for that.
*We need to be able to sell our currently equipped gear while we are in the shop menu. Having to close the shop, open the inventory, and then open the shop again can be a little frustrating from time to time.
*Tooltips informing that we already own "x quantity of that item" while buying something from a merchant.
*Mutagens of the same color should give higer/lower bonuses depending on what foe/monster they came from, the stronger the monster it came from, the higher the bonuses it should give compared to the regular ones.
*Trophies from stronger foes of the same type(Archgriffin for example) should give a better bonus than the trophies from the basic monster(Griffin).
*More unique art assets for trophies, in stead of re-using the "head on a bag" look for most of them.