the idea is good
but honestly, i just found it annoying. i couldn't even see that they were actually fighting, most of the time. the black ninja fighting black ninja on black background doesn't help much at all. i mean, it really just looked like they were gyrating around each other most of the time. the sound and dialogue isn't very good, either.
try making the ninjas different colors and making them fight inside a well-lit room or something. you could argue that ninjas don't fight in the light, but it would make for a better flash, my way.
i might also suggest making it a comic-book style, so you wouldn't even need vocal sound or dialogue. you could even make it look like an ancient chinese scroll or something.
basically, in a nutshell, while your 3d flash is great and all, it's hard to do a fight like that. try it in 2d until you find something that works.