After you train you have to eat to gain the skills/stats that you trained for, similar to real life. Certain restaurants and foods would benefit certain aspects of your strengths more than others. This would create for cool social situations at shops where everybody that trained can talk and such. This would also give purpose to having a ramen cart for example. Let's say you trained throwing kunai and you have to go eat to gain the boost. So once you're finished you now can throw kunai faster.

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If there are going to be bloodlines, there should be what I would call a "Family System." If you wish to be born into a bloodline you must contact a player that is already in that bloodline before making a character. (There would be a list of people in bloodlines.) Then upon consent on both sides, through a mail system, the new player can be born to the player already in the bloodline. Then in the new players info it would say what bloodline they're in and who their parent is. This system could allow for applying for certain bloodlines and seeing if your characteristics fit with the clan. If you are accepted you now receive the unique powers. This system would allow for families, that could battle for dominance. The head of the family could also be the final say in acceptances. Of course there would be a limit on how many children you can have. This system would create interesting clan history as the game progresses and filter out the nonserious players from having player specific powers.