A few ideas
I had a pretty lengthy response laced with ideas, but my internet went kaput and I lost all of my text, so I figured I would kind of throw out a shortened version of a few ideas I had been thinking on. They could prove completely useless and/or counterproductive, but I thought they sounded pretty cool, and may somehow spark some ideas.
Concerning Lotus Scourge: When I think ninja, I kinda think of...dart guns, and shooting poisoned darts from the shadows. Perhaps that upon selecting this ninjitsu, along with the upgraded poison, perhaps allow the ninja to, upon beginning combat from the shadows, to launch one, or a volley, of darts, as an autoattack. The damage would be miminal (scratch, graze), though, the target would be inflicted with the poison. Also, though I'm not sure how hard it would be to code it in, allow the Lotus Scourge poison to either replace a self-inflicted poison in the target, or even use the weaker, 1 or 2 hour poison, as a buffer, or stack, to the stronger poison.
Concerning Melee Abilities: I believe it was Croyvern's post I was reading, regarding different paths of ninjas, namely a melee ninja and an added defence. Perhaps, something similar to riposte, only instead of the damage done like a warrior, perhaps some different effects? Again, when I think of a ninjas fighting style, I think of deception, misdirection, and keeping the opponent off balance. The deception/misdrection could come in the form of some added defence, perhaps like a parry/sidestep, or some sort of feint, in which the ninja could utilize his superior position to sort of....nudge, or push, or some sort of strike, that would cause his opponent to lose balance a bit. Almost like a very, very slight lag attack. In some instances, maybe lag juuust enough that the ninja can get there flee off just before being bashed for the 2nd/3rd/4th time by the warrior he is engaged with. Again, the lag would be miminal. Just enough to allow the ninja a narrow escape, perhaps, or to keep there wounded opponent around long enough for one more trip/grapple.
Concerning a Magi Ninja idea: Perhaps, an ability that would allow the Ninja to infuse his blade with KI magic, lending it a minor damage boost, or some sort of extra attack(flaming/freezing/shocking bite, etc...). Or, perhaps, giving the ninja a sort of leveling ability for there weapon, similar to a Malform. The bonuses would be no where near that of a Malform, but just a small boost. Maybe cap the level out at 3 kills or so. Everytime the ninja dies, the blade loses its Magical enchantment. The bonuses won't be enough to make someone ragedelete after dieing, but enough to give the ninja a small boost in combat.