Ok, here a little Alternate Version of my proposal, based on 4 Mudras
Ten, Chi, Jin, Rei/Wol
Changes:
The Term Chakra becomes then instead again Ninki, but the way it works/is balanced cost wise, gets reworked.
All Ninjutsu cost now Ninki, Like mentioned, skills get integrated into the Mudra System.
1 Mudra Skills cost 10-20 Ninki
2 Mudra Skills cost 25 to 40 Ninki
3 Mudra Skills cost 50 Ninki
4 Mudra Skills cost all Ninki and can either be used only at Max, or are potency reliant based on the amount of Ninki you had at the moment.
Traits and specifit skills will make sure to generate a quick enough flow of regaining Ninki, so that you can perform often enough Ninjutsu to make good DPS
Lvl 45
Han > Rei
Lvl 50
Again only Kassatsu
Level 62
Kuchiose Magikai Joou replaced with new Skill "Explosive Daggers" > Throw a pair of Kunais enhanced with Fuin Bakahatsu, which will explode on enemy contact, dealing Aoe Damage. A direct Upgrade for Throwing Daggers (Kunais)
Additional new Trait: Master of Explosive Seals: Upgrades Throwing Daggers into Explosive Daggers
Lvl 78 Trait Healthy Chakra renamed to Stamina Mastery
Changes to Formulas:
1 Mudra Skills
Ten > Fuuma Shuriken/ Fuuton: Rasen Shuriken
Chi > Smokescreen/ Suiton: Yasui Kirigakure
Jin > Death Blossom/ Raiton: Chidori Senbon
Rei > Shukuchi/ Doton: Hossori Kage Bunshin
2 Mudra Skills
Ten Chi > Hyouton: Tsubame Fubuki
Ten Jin > Katon: Fuin Bakuhatsu > Fuin Kai
Ten Rei > Raiton: Kuchiose Hebi Mikatsuchi ( Summon Lightning Snake), deal strong damage to single target with additional Poison DoT if heath is over 50%
Ten Ten > Fuuton: Yoroi Arashi
Chi Ten > Katon: Goka Mekkyaku
Chi Jin > Suiton: Kuchiose Magikai Joou > moved from Lvl 62 Skill to here.
Chi Rei > Doton: Ryuusa Torappu
Chi Chi > Mokuton: Seikatsu no Tsurii
Jin Ten > Fuuton: Kuchiose Kamaitachi
Jin Chi > Doton: Maisoo no Tsumi
Jin Rei > Hyouton: Hyosho Ranryu
Jin Jin > Raiton: Raikyuu > Sends out a slow flying Ball of Lightning that damages over time all foes in line of sight
Rei Ten > Suiton: Ame San
Rei Chi > Mokuton: Moku Jouheki > A defensive Ninjutsu, that protects everyone inside the Wood Shell from damage, which gets reduced by 20% and makes all inside immune to launches and other CC effects, exceptions may exist
Rei Jin > Katon: Kuchiose Gamabunta (Hellfrog Medium)
Rei Rei > Raiton: Doshaburi Raisen
3 Mudra Skills
Ten Chi Jin > Ninpou: Yume Ananta Mono no Yume
Ten Chi Rei > Ninpou: Hageshiku Buki
Ten Rei Chi or Ten Rei Jin
Ten Jin Chi or Ten Jin Rei
Ten Ten Chi, or Ten Ten Jin, or Ten Ten Rei
Ten Ten Ten
Chi Ten Jin > Ninpou: Koutai
Chi Jin Ten
Chi Ten Rei or Chi Rei Ten
Chi Jin Ten or Chi Jin Rei
Chi Chi Ten, or Chi Chi Jin or Chi Chi Rei
Chi Chi Chi
Jin Ten Chi
Jin Chi Ten
Jin Ten Rei or Jin Rei Ten
Jin Chi Rei or Jin Rei Chi
Jin Jin Ten or Jin Jin Chi or Jin Jin Rei
Jin Jin Jin
Rei Ten Chi
Rei Chi Ten
Rei Jin Ten or Rei Ten Jin
Rei Chi Ten or Rei Chi Jin
Rei Rei Ten or Rei Rei Chi or Rei Rei Jin
Rei Rei Rei
With this becomes clearer how much more versatile this concept is compred to the current Ninja, due to alot more Ninjutsus to use, making playing this class good feel alot more rewarding, if yo can make situationally best use out of them all, and all of that by making just only combinations with 4 skills.
Sure havent thought about so many new skills yet, but I wanted to give also some free room for SE's creativity to fill the gaps ^^
Any other non named formulas will count as mistake, means you summon the Rabbit on your Head
4 Mudra Formula
Here exists only one and that would be (otherwise too complex)
Ten Chi Jin Rei
PS: Thats also the good thing about the Ninja, even if you don't know exactly all formulas in and out, theres this aspect of funny randomness in this mechanic to basically press any random formula, and you still receive in 90 pecent of all cases a useful skill, so I see no big deal for it to increase with Mudras the amount of usable ninjutsus for PvE.
It would makes Ninjas also in Pvp more fun, because you'd be completely unpredictable there with a higher amount of Ninjtsus, other than only basically 4 to 5
Ninja should be a class thats easy to lesrn but hard to master. Much more Ninjutsus are therefore neccessary for a better versatility.