So as we all no doubt know that skills are getting a revamp. Shared skills will be role based instead of class based (sounds scary. I like classes) and ineffective or unused skills will be reassessed.
Since I've had ninja as a main since 2.4 I figured I will give my oppinion on what changed ninjas might need. And naturally you can and should do the same here.

General ideas:
- Don't overdo ability pruning!
The very reason I decided to quit wow forever was the overdone ability pruning in legion. You sometimes don't get a single new ability or talent point for 8 levels. Heavensward already moved away from class skills and traits (a very bad move in my oppinion). I like to get new tricks when I level up.

- Ninja doesn't feel more ninja enough.
The shortage of armor and weapons actaully fitting the ninja might be partially to blame, but outside of the job quests, fuma shuriken, shukuchi and suiton, ninja isn't that ninja like at all. We jump, we slash, we throw around very visible elemental spells. We need more traps or perhaps transformation. That fourth mundra could have several aplications.

- Combat isn't varied enough.
By the time I finish refreshing Shadow Fang, Dancing Edge, Mutilate and Huton (With armor crush) I pretty much have to start again from the beginning. If I don't, my dps drops. It would be nice to increase their duration to give us more time to try out the new tricks that we will hopefully get in Stormblood.

Now on to useless skills

- Throwing Dagger
This is a special case as it really IS useful for rogues considering this is their only ranged skill, but after the job change I really really really don't use it much. Most of the time the enemy is in range of Raiton anyway or closer. Far closer.

- Fuma shuriken
Another special case. It is the first ninjutsu skill we get and one of the very few that actually makes you feel like a ninja. But sadly it's not really that useful in a fight. It's longer range doesn't see much use with ninja being a melee class and all, and even Katon hits harder. For AoE damage. It is supposedly stronger than Raiton if you have Dancing Edge, a Machinist with Hypercharge a poison and bad latency, but that is a very big IF. I like the look of finishing a boss with a huge ninja star so I tend to throw one at bosses at 1% health, but that's for show. Besides it has 3 different mundra combinations. It might be better to turn those three into three diffferent kinds of shuriken with more creative effects. Mundra combinations in general are a good way to give us more skills withouth filling the action bar. Give a short range shuriken with knockback or a Mortal Kombat style kunai with a lance to draw in enemies, or a shower of smaller shuriken for AoE damage. Anything.

- Poisons
Kiss of the Viper and Serpent are very very boring. Usually I apply them at the middle of duties because I just forget about them. Or rather forget that I have to reapply them after every level synch. They give a 20% damage bonus so they can't be ignored but their interaction with other abilities is very limited and again, they disappear with each level synch. They are like bullets only worse in every regard. Using poisoned blades fits both rogues and ninjas so removing them might be bad, but they definitely need rework.

- Smoke Screen and Shadewalker
These two that we got in Heavensward are nice on paper because they are good for aggro management and even fit the job fantasy, but they just don't find much use in fights. Obviously they never come up in solo play ever and even in duties only if the tank is very bad or very dead.

- Hyoton
I literally forgot that this skill even exists. Technically it doesn't take up hotbar space, but really I have to remind myself that I have it.