Ninja has started out this expansion being exceptionally weak. I've been reading some of the other forum posts about ninja and I've noticed that no one seems to mention Huton. It is a pretty redundant skill to keep up. 15% skill speed basically? That could literally just be a ninja passive. Most of the ninja passives are worthless ninja flare skills. Run like 1% faster, take 1% less falling damage, etc. Why don't we have more combat oriented passives instead of these wastes of space? There's so much that could be added there. I think Huton's current effect should be moved to the passive skill section which could be titled Kaze no Gotoku (like the wind) or Ninja Reflexes or something like that.
What if you were to give Huton the effect of having a % chance of causing your attacks to double hit? That would add a fun element of randomness to it. Make it work like a passive mini Bunshin effect, where Huton gives you 30%~ chance for your weapon skills to proc twice, enhanced appropriately by position and combo, like how I believe Bunshin should function. It doesn't have to apply the dot from Shadow Fang but the weapon skill damage should be mimicked. (Bunshin probably shouldn't benefit from Huton procs, so you'd see a total of 3 weapon skill damages if you had a Huton proc while Bunshin is active.)
Then on to the issue of ninki, the skill usage window is so small that it's just not that enjoyable to use. If you were to lower the threshold on the ninki skills to 70, that would help with the skill usage window and would also provide a nice slight damage increase to ninja as well.
I think with these changes it would make ninja feel even more active, where you're getting to use your ninki a little more often, emulating the attack speed of dual wielding weapons. This in turn would improve the dps of the class by a fair amount, making them feel like a more competitive class while not simply tuning the potency of their abilities. It would be super fun and active, allowing the complexity of the class shine.