I think the idea is pretty good over all. I have been thinking about ninja paths for a long long time. This is what I have always leaned towards.
Melee Path: Still stealthy but melee oriented. Stronger melee ability than say a thief or bard, but not as powerful as warrior/monk/blademaster.
Abilities would include: Side-Step (About as defensive as parry), Shadow Arts, and Doublesheath.
Stealth Path: Keep Study and Assassinate, can ONLY study and retain it out of combat. making it more difficult to be an "oops I got him" or "Hahaha I ran circles and got you" assassin. Make study take a bit more ability, like straight lines perhaps? Maybe give them a way to put people to sleep even if they are poisoned, and make assassinate only work if that person is asleep.
True Rogue Path: Get an upgraded form of poisons/blindness dusts and plague dust. Upgrade nerve for them, tie grapple into an "air thrash" type of ability, pulling them out of the air and onto the ground for caltrapping. The path would be entirely dependent on doing things right. Like a thief, you do it wrong and you're gonna be lagged to death. Give them improved vanish to make it a bit easier to get out of "sticky" situations.
I dunno, I hate the stealth aspect of ninjas for the reason that I feel that thieves are more of ninjas than ninjas are. Ninjas were assassins but good enough fighters to take on samurai, which are like the bad-asses of the fighting world...It just doesn't really add up to me.