Skills change: The way I've been looking at ninjas is kinda the same way I've looked at monks/blademasters. Screw assassinate. Gearing a class around one skill is kinda retarded. They have awesome skills for fighting, I just see them a bit low on defenses. Don't give them something ridiculous like twohanded or shield block, but I believe they should get a defense that makes the ninja anticipate an attack, avoid it, and strike a vital organ. This skill if mastered is always about a 25% probability that it would ever land. A way to make this skill more interesting would be to change study. But if you study someone, say Crypticant, and their soul bears your mark. You recognize their movements and habbits, hence making your defensive strike more of a 50% chance of happening in a round. Hence making study useful.
Another change you could look into is making them a bit more geared to trickery. Something such as an ability that draws your enemies attention, such as a lolly pop, who wouldn't want to pick one of those up? Then bam, ambush from the shadows, OUCH that hurt like a mofo. Not so much like backstab or anything like that, but maybe a traumatic strike to your kidneys. I mean really, who likes peeing blood?
This would make ninjas still geared towards being sneaky and using study, as well as being tricky and using diversions. Then choosing the right ninjitsu suited for you would make you a worthy adversary against people like those bash/bodyslam locking bastids. I dunno, maybe I went over the top with them, but that's the way I always saw ninjas.
Reading over some old ninja threads this one I must've over looked because I immediately got a few more ideas from your original post. Altering the study skill to increase the effectiveness of certain skills and attacks seems like a great idea. I can definitely see how studying a target may increase the effectiveness of shadow arts allowing you to hit critical parts of the body for more damage or more varied effects i.e. bloodloss, paralysis, lack of concentration. Or maybe since you know more about their weaknesses and the way they move your throw skill could do more damage as you murder or as they turn to flee since you'd be more certain to hit them in more critical areas.
Haha that lollipop ambush idea is hilarious but it seems awfully similar to the traps thieves have. The idea of creating object and leaving them on the ground as a trap seems like something the thief is more geared towards but is a fun idea nonetheless.