(I may be wrong in part of this. Please correct me if this is the case.)
When creating a character you are allowed to pick a type of fighting to specialize in. Picking taijutsu(strength) allows you to have an extra attack while fighting that also increase the speed you gain taijutsu and increases your starting taijutsu stat. Picking ninjutsu or genjutsu only increase your starting stat for each and nothing more. There's also balanced, but I don't have much experience with that. (Increases starting levels for all?) With the specialize system like this there's no point in picking anything except taijutsu. Here's my solution to this:
Ninjutsu - Increase the damage of their ninjutsu attacks. (No more than 1.5x)
Taijutsu - Same, but maybe add slightly more damage to taijutsu attacks if this becomes inferior to the rest.
Genjutsu - Increase the time their genjutsu attacks last. (Only like a second or two.)
Balanced - Umm....all the above affect, but decreased. (For example, a ninjutsu boost of 1.2 while choosing to specialize in ninjutsu gives you 1.5x)