As there are five elements a jutsu can be (Earth, Fire, Water, Wind or Lightning), and many ninjas have an affinity for one of those elements in their jutsu, I propose a system that would give each person one random elemental affinity. Upon reaching Jounin rank or the Wandering Ninja equivalent, that person would be assigned, at random, one of those elements. When using a jutsu of that element (Fire = Katon, Wind = Fuuton?, Earth = Doton, Water = Suiton, Lightning = Raiton?, Chidori), it would increase in power by 50%. Of course, this would present some obvious problems. If a character was a Jutsu Specialist and only knew Fire Jutsu and had an affinity for Water, it wouldn't make much sense. So perhaps the person could choose their element or it would be given to them based on what attacks they knew?
This could also be a building stone for jutsu based on what village you came from. If you came from Leaf, Katons. Mist, Rain, or Waterfall could get Suitons. Raitons and Fuutons haven't been shown yet, but Sand would get Fuutons, I assume Cloud would get Raitons, no idea about Sound, and Grass and Stone would get Dotons. This is just a suggestion, and I don't want bashing but constructive criticism is much accepted.
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