It depends on the reason. The characters may be missing nin, or simply a task force from a variety of the governments- depending on what sort of stories we're planning on doing. God knows, though, even in one village there's a great enough amount of diversity- even assuming that the Hidden Leaf has one of the most varied compositions of ninjas, there's dozens of specialties that they have. I'd definitely be interested in such a game, by the way- Either Freeform or system, though I do enjoy systems just because they make combat a lot easier.
And hey, I could get my head around Rifts- I think I can deal with a few new charm trees
Leaf: Shadow jutsu, binding another's shadow. The Sharingan, capable of copying another's movements perfectly, and at higher levels, some really silly shit. Size changing, which usually burns massive amounts of calories. Mind switching- slow, and leaves them somewhat vulnerable, but useful for spying. Byakugan, perfect vision, apparently in distances of hundreds of meters in the stronger users, and high control over their own chakra. At least one character is incapable of molding his own chakra, but has compensated by becoming utterly, frighteningly powerful at Taijutsu- hand to hand combat. Bugs. Dogs. And a rare ability to use Wood jutsu, combining Earth and Water abilities. Lots of possibilities obvious.
Sand: Puppeteers, who tend to fight through proxy, and a high level of control over wind.
Water: People with mother fucking huge swords, and little to no regard for human life.
And in general: Demon-bonded, though they might be a bit overpowered compared to the others, Medical ninjas, etcetera, etcetera.