#3 is an idea I can get behind. This reduces the margin of error and allows for more flexibility in what you use under Ten-Chi-Jin. Locking Ninjas in place would be a good counterbalance to such a powerful ability.

While I would be fine with change #1, I don't think it should have charges. I don't like Kassatsu with charges, so having the basic Ninjutsu with charges wouldn't make this better. Additionally, suggestion #2 confuses me since Kassatsu already resets your Ninjutsu cooldown.

I think at this point, Ninjutsu should generate the Ninki, not the GCDs (or Auto-attacks) since Ninjutsu was Ninja's main gimmick before Ninki. Let one gimmick feed into the other. Adjust the amount of Ninki generated depend on the Ninjutsu cast (so Raiton generates a lot, Katon depends on targets hit, Suiton doesn't generate much since it's useful for something else, Huton generates depending on how much Huton timer you have left, giving you something to do during down time)

Kyoton needs to be changed. The idea of the Kassatsu upgrade was interesting, but it doesn't fix the problem of Kyoton itself. I was thinking Kyoton gets remade into a single-target DoT that can be refreshed by something like Armor Crush or a new GCD.

Trick Attack potency lowered but duration increased would make sense. Chain Strategim and Technical Step both last 15s.

Meisui was an interesting idea but functionally useless since it only dispels the Suiton buff. It seems like a skill you want to use during downtime but you can't since you can't hit anything with Suiton to get the buff. If it was so that you input the mudra for Suiton, you could hit Meisui instead and get the Ninki that way. However, this seems kinda moot with the Ninki/Huton change I suggested above.

I don't think, however, Ninja should do as much damage as, say, Monk. Monk, at the end of the day, is an overall more difficult job to use. Maybe if it was more in line with Dragoon, if somewhat behind, then I feel Ninja would be in a good spot pDPS-wise.