Weapons, Classes and Mutations - There are some things missing

[Matt__AsA__Hatter]

Lets start by examining the current systems

Weapon Types:
Dual Wield (Slashing/Pierce) - needs a blunt style, like boxing gloves made out of stone/sap
Bow (Pierce) - has elemental arrows and such to solve issues
Staffs - has all elements to work with
1 hand (Slashing/Blunt/Piercing) - has one of everything
2 hand (Slashing/Blunt) - needs a piercing style, 2 hand spear that cannot be thrown, like a weed stem with something attached to it

Classes:
Rogue: Uses Dual Wield
Ranger: Uses Bows
Mage: Uses Staffs
Warrior: Uses 1 hand weapons with shield
So who is to use the 2 hand weapons?  There should also be a class that is focused around them.  Possibly a Barbarian of sorts.

Mutations for Weapons:
Lil Fist - Works with NO weapons
Assassin - Works with ALL Dual Wield (Daggers and Sickles)
Sharpshooter - Works with ALL Bows
Whittle Wizard - Works with ALL Staffs
Smasher - Works with Blunt weapons
Javelineer - Works with Spears
Blademaster - Works with Swords

Problem:
What this means to someone playing is that if you are a Rogue, Ranger or Mage player then there is only 1 choice for what to pick to get benefits from all weapon options.  Where as if are a Warrior you must instead choose to do 1 hand weapons with a shield or a 2 hand playstyle and you also must choose between the 3 options of Smasher, Javelineer, and Blademaster.

Suggestion:
Lean into what you did with actual classes.  You already have paired up the Rogue, Ranger and Mage.  Split the Warrior into 2 seperate classes that have their own identity as a Fighter type with 1 hand with a shield and a Barbarian type that does the 2 hand weapons. 
Adjust the Mutations a bit so they pair with a class instead of a weapon type.  Blademaster could stay and be only for 1 hand weapons.  Keep Javelineer and let it also be for 1 hand weapons to motivate people to do a thrown weapon style of play if they choose to.  Then put Smasher into 2 hand weapons and possibly come up with another choice for them too.  The names would likely have to change but their functions could stay the same.  Blademaster > Stami-Master, Javelineer > Relfecter, Smasher > Stunner, just the first things that popped to mind.
If you give 1 hand weapons 2 choices, you could give all players more than one way to build with their desired weapons.  Dual wield could absorb Lil Fist or could have bleed or poison instead of just crit.  Mages could do more hit based damage instead of scaling the elemental effects.  Rangers could maybe do bleed with the bows via mutation, or also more crit like dual wield.  There's tons of options I could ramble about and plenty to choose from to give the players more choices in how they want their class to work.