If they are normal ninja, or perhaps a cross with something like Ninja Cadets... I might read it to see how the problems doing this to their characters might be resolved with the NGE storyline.
If this is a Naruto cross and that type of ninja... no. For me, that is what some might call autofail.
The problem with the concept as a whole though, is the why of it. Gendo's and Seele's plans both rely on pilots being in the dark, and being either eager enough to serve without question (Asuka), or emotionally distraught and blackmailes and brought up with so little spine as to question anything (Shinji), or basically manipulated from birth for complete loyalty (Rei). If you do this, how would control be done, or if they know the truth, why they would still follow.
Additionally, if they are made Ninja (of any type), there is the fact that since to fight angels, how would the abilities benefit them in combat?
So... if Gendo and Seele would have no need of them being Ninja, in fact have reasons to not do so, then they would have to become it on their own. Ok, I can see one, possibly two, but all three do so, when they had no contact with each other. Maybe if a rival to Seele/Nerv knew the kids would be manipulated, they might approach the kids and train them. But that still leaves how, as while it might be easily done for Shinji, Asuka and Rei were brought up on Nerv bases, under likely constant guard.
Now, one could ignore all the above issues, and change the plot and backdrop so it fits... But then, with changes that widespread to character, motivation, personality, and backdrop... would it still be an NGE story?
