NarutoMUD

Every character has a different personality which makes them different from one another. But Personality also has an effect on how people do things as a whole.. Certain traits i believe could futher strengthen character devlopment icly and simply just running around in the Mud. Traits can effect things from prices in the shops to the strength in their muscles... Heres some Examples...

A Natural Learner - Learn jutsu a bit faster than usual

Determined - Never willing to give up possible adrenaline rush during life threating situation - extra recovery from exhaustion?

Strong Willed - Lscing wisdom comes easier.. No one can break your Will

Flexibile - Dexterity Lscing or even stat bonuses..

Those are just a few examples of traits... How they can be obtained I would think would be quest based... or Koto style.
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Specialization

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Certain people work at things long enough until finally they become a natural and super adept to it.. knowing things better than anything else could effect how certain skills are used... or add bonuses to the skill itself. Example

Taijutsu Specialist - Limited in Ninjutsu - increase speed of Taijutsu skills by X percent..

Katon Specialist - Significant Speed boost in fire type jutsu - Or - 10 Perecent less chakra required to use fire type jutsu
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It can go along those lines.. Specality can come at certain levels... Each one having their odds and ends.