Here are my ideas for how they will / how I would handle Ninja.

Simplify the weaponskill combos. New combos would be Spinning Edge > Gust Slash > Aeolian Edge and Spinning Edge > Armor Crush > Shadow Fang.

OR: Remove Huton and make it a always on trait, and make the weaponskill combos Spinning Edge > Gust Slash > Aeolian Edge or Shadow Fang. Similar to War's combos.

Leave the skill Ninjutsu as a oGCD ability with a 1s CD that changes Spinning Edge, Gust Slash and Aeolian Edge into Ten, Chi and Jin respectively with a 1s or 1.5s GCD. Once you have a Mudra combo ready you use the Ninjutsu ability to use that combo and put Ninjutsu on a 20s CD. Potency's would need to be increased but probably not DNC levels.

Make Weaponskills give maybe 5 Ninki while Ninjutsu give 10 or 15 to spend on Ninki spenders. (I've always just viewed Hellfrog Medium, Bhavacakra, and Bunshin as advanced Ninjutsu so in my mind Ninjutsu should give Ninki.)

You could also change Ninki to be more like Aetherflow where your Ninjutsu give you a Ninki charge to spend on Ninki Spenders.

Permanently upgrade Katon and Hyoton into Goka Mekkyaku and Hyosho Ranryu.

Remove charges from Kassatsu and make it so it triggers Ninjutsu so your weaponskills change to Mudras and makes your next Ninjutsu a Critical Direct Hit. (So no need to hit Kassatsu > Ninjutsu.)

Have Ten-Chi-Jin do the same thing it does now EXCEPT it now changes your weaponskills into Mudras and allows you to move. (So no need to hit Ten-Chi-Jin > Ninjutsu.)

Remove Trick Attack and Suiton and make Ninja all about the Ninjutsu. (Yes this makes NIN more like SAM but they would still feel really different to me.)

OR Remove Trick Attack and make Suiton a party buff like Technical Step. (Yes this makes NIN more like DNC which is why I say remove it.)