I’m intersted to see what type of bonuses you want to add and/or change. Here’s what I would do for each skill classes considering there are only 11 skill modifiers for each class, with the exception of adding Necromancer since they have 12.
Shaman:
Add Conjure Primal Spirit bonueses by giving them either Aether or any other damage modifiers besides cold since it is not included.
Change: Lightning Summon Briarthorn by giving them Aether, chaos or pierce bonuses, as there are many skill modifiers that have the same damage type, except for Aether versions for pets besides Wardens judgement.
Conjurer:
Add: Physical or Lightning bonueses to Sigil of Consumption.
Change: Chaos Summon Hellhound bonus to support Aether version, as again, there are many pet items that support other damage conversions besides Aether.
Arcanist:
Add Acid AAR, considering it is the only damage modifier left that has no conversion
Change: OFF into a retal version on attack with Callistor Tempest considering it’s not a usable skill endgame.
Nightblade
Add: Blade spirit conversion into acid, chaos or aether
Change: Blade trap with something more useful such as Aether ABB or Chaos Phantasymal blades
Soldier:
Add: Counter strike to cold damage since there isn’t an item for it
Change: War Cry with pierce or bleed Counter strike since there isn’t an item for this (just yet)
Necromancer (note, it has already an extra skill modifier while the others only have 11
Change: Fire raise skeletons with Aether damage
Inquisitor
Add: Aether inquisitor seal modifiers from the Bonemonger set as it has been replaced by the skills related to Word of Renewal for 1.3
Change: Vitality Rune of Haggard and replace it with the inquisitor seal modifiers replaced on the hood of Bonemonger set
Demolitionist
Add: Chaos Fire strike
Change: Acid Fire strike to Aether blackwater cocktail
Oathkeeper:
Add: Eye of Reckoning to chaos or aether (as mentioned)
Change: Summon Guardian of Empyrion’s target area in terms of resistance from Aether and Chaos considering Bonemonger has it to replace it with Pierce and Bleed


