Do you like to bruteforce alchemy ingredients each time you visit a lab ? Do you like having millions of potions with the same effect but different magnitude? Do you feel that alchemy should force you into some investments into perk tree & ingredients? Do you feel that removing spell crafting was a wise decision from Bethesda? If the answer for last two is "Yes" and for others is "No" then you are in the right place. Probably

Vanilla alchemy system is completely disabled. You can't mix & match ingredients and create custom potions anymore. Instead you can craft Vanilla Potions (and possibly mod added potions if they are correctly tagged via KID. Support for Apothecary is built-in).

All potions are divided into 5 tiers following vanilla (note: some potions/poisons have only 4 tiers and starting from Apprentice):
Novice
Apprentice
Adept
Expert
Master

Tagging is done through Keyword Item Distributor config.

Without any perks you can craft only Novice potions. You can take a perk to craft higher level potions at 20, 40, 60, 80 levels of alchemy. To craft a potion you must:

• Have appropriate perk for potion level 
• Have 2 ingredients with the same effect
• Know effect from both ingredients. 
  

Accompanying SKSE plugin automatically generates potion & poisons recipes at runtime based on ingredient effects & ingredient rarity . 

All ingredients are divided into 3 rarity tiers (Mostly following vanilla LItemApothecaryCommon/Uncommon/Rare items list):
Common (flowers, wheat, etc)
Uncommon (most mushrooms, monster ingredients and similar)
Rare (fire/frost/void salts, daedra heart, rare fish, etc...)

Tagging is performed through KID config. In case of unknown ingredient (e.g. mod added) the plugin assumes that it has Uncommon tier. Vanilla, CC AE content and Apothecary support has built-in.

Additionally the plugin automatically appends rarity suffix (configurable, default ON )  to the ingredients so you would know what to sell and what to keep for better times ;). You can adjust names or disable this feature completely in AlchemyReworked.yml file

Taking both list of potions & ingredients, the plugin generates potion & poison recipes based on following rules:

• Common Ingredient + Common Ingredient           = Novice
• Common Ingredient + Uncommon Ingredient       = Apprentice
• Common Ingredient + Rare Ingredient                   = Adept
• Uncommon Ingredient + Uncommon Ingredient   = Adept
• Uncommon Ingredient + Rare Ingredient               = Expert
• Rare Ingredient + Rare Ingredient                           = Master
  

You can configure these rules as you like in AlchemyReworked.yml config
So to create good potions you must have invested into getting proper ingredients. Experienced alchemists can create slightly better potions from the same ingredients when taking appropriate perks:

• Benefactor - You create now one level higher potions from the ingredients.
• Poisoner - You create now one level higher poisons from the ingredients.
• Purity - All created potions and posons will be one level higher. Stacks with Benefactor and Poisoner.
  

These perks automatically "bumps" potion level by +1 to max +2 (for both Benefactor/Poisoner + Purity). That means that you will get Apprentice-level potion from common + common ingredient with 1 perk and Adept-level potion with 2 perks. And Master-level potion from 2 uncommon ingredients, so it's a good investment :)

Almost all mod work is performed at runtime in SKSE plugin in compatible and conflict-free way. Accompanying ESP is needed only for perk/tree changes because old perks for alchemy effectiveness don't make sense anymore. 

Recommended mods:
Apothecary or similar. It's not required but very recommended to adjust and normalize potion & effect values. Without it few novice level potions will have high price making it's too easy to get money. Additionally it's adding few interesting effects which are supported by my mod
Alchemy Recipe Expansion and Recipe Auto-Learn . Since it's not possible to bruteforce ingredients anymore to learn effects you either should resolve to perks or as true alchemist to recipes. Highly recommended to get both. 
Few players also recommended this mod . I personally don't use this mod but having more available ingredients won't hurt i suppose

Compatibility:
ESP plugin is only touching Alchemy Perk Tree and few perks to make sense for new alchemy progressions. Perks effects itself are not important (and I deleted associated effects from them). If you don't like my changes you can overwrite it with other mod. However you need to open SKSE/Plugins/AlchemyReworked.yml and provide Form IDs of perks which will be responsible for alchemy progression:
perks:
  # Perk to enable apprentice quality potions
  level2: Skyrim.esm|BE127
  # Perk to enable adept quality potions
  level3: Skyrim.esm|C07CA
  # Perk to enable expert quality potions
  level4: Skyrim.esm|C07CB
  # Perk to enable master quality potions
  level5: Skyrim.esm|C07CC
  # Perk to make potions +1 quality
  potionQuality: Skyrim.esm|58216
  # Perk to make poisons +1 quality
  poisonQuality: Skyrim.esm|58217
  # Perk to make both potions & poisons +1 quality
  allQuality: Skyrim.esm|5821D
  # Perk to increase produced potions & poisons by +1 (not exist in vanilla game but perk overhauls often add it)
  doubleItems:

For example here is from Adamant patch:
perks:
  level2: Skyrim.esm|BE127
  level3: Skyrim.esm|C07CA
  level4: Skyrim.esm|0C07CB
  level5: Skyrim.esm|C07CC
  potionQuality: Skyrim.esm|58216
  poisonQuality: Adamant.esp|DA3D2
  allQuality: AlchemyReworked - Adamant Patch.esp|A01
  doubleItems: Adamant.esp|DA3D3

Adamant , Vokrii - Minimalistic Perks of Skyrim and Vanguard Path - Rogue Gameplay and Perk Overhaul patches are provided in optional files. Load main file BEFORE perk overhaul and patch AFTER

Vanilla Perk Changes:


Vokrii - Minimalistic Perks of Skryim Changes:


Vanguard Path - Rogue Gameplay and Perk Overhaul Changes:


Adamant Perk changes are mostly similar to the vanilla perk changes above. I've added new Perk (Purity, for +1 potion/poison level), restored "Experimenter" (eating ingredient reveals N effects) perk levels (reasoning - to smooth progression, otherwise there is no point in buying recipes) slightly rearranged alchemy tree and repurposed existing perks to follow new potions progression

Source Code 

License: MIT

Credits
powerofthree / Crafting Recipe Distributor for example how to create native COBJs from SKSE plugin