If you had to remake your job from scratch...

[Khalithar]

Ninja:

Remove positionals.
Huton becomes a passive.
Turn Trick Attack in to a one minute cooldown attack.
Make Suiton apply a DoT.
Upgrade Hyoton/Katon in to their Kassatsu versions permanently once you reach high enough level.
Turn Kassatsu back to it's old version (auto crit).
Remove Shadow Fang/Armor Crush.
New animations for the base weapon skill combo that are more... Ninja-like if that makes sense.
Weapon skills no longer cause bunny on Mudra cast.
Messing up your Mudra combo (if your finger slips or whatever) causes the chain to reset and the bunny effect can no longer happen.
Make the little Mudra bunny a separate emote.
Let me decide which Mudras to use during Ten Chi Jin, I liked being able to do Shuriken/Katon/Doton during trash pulls. I'm not a fan of being locked in to Shuriken/Rai/Sui. Also, make the Ten Chi Jin have a 1 min CD with the DoT from Sui above lasting 60 seconds.

That would make Ninja perfect to play as far as I'm concerned.