I use the brewery recipes and potions in a fantasy way. The brews give enhancements and are non-alcoholic. One of the things I think would be amazing for PvP would be the inclusion of some sort of Achilles' heel. Where 1 player can drink Rock brew and will be vulnerable to attack from someone who drank Paper brew, but be better at fighting someone who drank Scissor brew. All 3 players would be more vulnerable to someone attacking them who drank Bane brew. Essentially, when someone has consumed a brew that is the achilles of the brew you drank, they can kill you with ease, regardless of any status effects you may have.

The individual recipes can include a line, " achilles:" in which the name of 1 or more brew name can be placed. I'm not sure how a player who drank X brew could be marked as having drank X brew for a variable length of time. A line called "markedtime:" could be used to indicate how long a player is to be set as having drank X brew.

Here's an example of what such recipes would look like if able to implement:

,,,
1:
name: Rock
ingredients:
- STONE/5
cookingtime: 3
distillruns: 2
wood: 1
age: 1
color: RED
difficulty: 3
achilles: Paper/Bane
markedtime: 600
effects:
- DAMAGE_RESISTANCE/14/1638
2:
name: Paper
ingredients:
- PAPER/5
cookingtime: 3
distillruns: 2
wood: 2
age: 1
color: BRIGHT_GREY
difficulty: 3
achilles: Scissor/Bane
markedtime: 600
effects:
- HEALTH_BOOST/19/1638
3:
name: Scissor
ingredients:
- IRON_INGOT/5
cookingtime: 3
wood: 3
age: 1
color: CYAN
difficulty: 3
achilles: Rock/Bane
markedtime: 600
effects:
- INCREASE_DAMAGE/10/1638
4:
name: Bane
ingredients:
- SKULL/5
cookingtime: 3
wood: 3
age: 1
color: BLACK
difficulty: 3
markedtime: 1638
effects:
- WITHER/6/1638
,,,

Another idea to couple with this. A particle trail setting. I know some plugins allow players to turn on particle trails like fire sparks, lava, ender portal particles, etc all of which trail behind the player a bit and disappear. Having a setting in the recipe and a timer specified would be great for the above idea. When someone sees you running around they will know what type of potion you drank and know what potion will counter it. Examples:

,,,
1:
name: Rock
ingredients:

• STONE/5
  cookingtime: 3
  distillruns: 2
  wood: 1
  age: 1
  color: RED
  difficulty: 3
  achilles: Paper/Bane
  markedtime: 600
  particle: smoke
  particletime: 600
  effects:
• DAMAGE_RESISTANCE/14/1638
  2:
  name: Paper
  ingredients:
• PAPER/5
  cookingtime: 3
  distillruns: 2
  wood: 2
  age: 1
  color: BRIGHT_GREY
  difficulty: 3
  achilles: Scissor/Bane
  markedtime: 600
  particle: enchantmenttable
  particletime: 600
  effects:
• HEALTH_BOOST/19/1638
  3:
  name: Scissor
  ingredients:
• IRON_INGOT/5
  cookingtime: 3
  wood: 3
  age: 1
  color: CYAN
  difficulty: 3
  achilles: Rock/Bane
  markedtime: 600
  particle: crit
  particletime: 600
  effects:
• INCREASE_DAMAGE/10/1638
  4:
  name: Bane
  ingredients:
• SKULL/5
  cookingtime: 3
  wood: 3
  age: 1
  color: BLACK
  difficulty: 3
  markedtime: 1638
  particle: reddust
  particletime: 1638
  effects:
• WITHER/6/1638
  ,,,