Dude... Great list, but so many missing ninjas...
What about...
...Edge from Final Fantasy IV? he is the lord and master of an entire ninja village, so badass he goes "super saiyan" and unlocks all of his level-up abilities at once because some flasher pissed him off.
... Strider Hiryu? ninja technomancer of the future, slicing and dicing enemy cyber-ninjas and giant maverick robots. Speaking of which...
... X? in Megaman X6, X gains access to the ninja Shadow Armor, that lets him shoot shurikens and powers up his beam saber, and is arguably the most powerful and useful suit next to Ultimate. Kirby's in, so why not?
... Zelda? Her Sheikh persona in Ocarina of Time (and Super Smash Bros) shows off Zelda's badass physical skills as well as her powerful magic.
... freaking Hanzo Hattori? historical forefather of all Ninja and badass infiltrator/assassin from the Dynasty/Samurai Warriors series.
...any or all of the ninjas from League of Legends: Akali, Shen, Kennen, Zed, Katarina, Talon... the list goes on.
