Heres my suggestion on 'special' (special nature type) kekkei genkai.
Here's how I think it should work.
For every X amount of unique player account that has one character reach a certain overall skill level or player level (if you're having those in this game), one random person out of those X amount of peoples shall be chosen to have this special nature type.
Here's an example.
1500 people are playing the game, for each 100 people to reach a certain level over all for their character, one person out of the 1500 shall be chosen to have a special nature type (this could obviously be different, it could be for each 500 people..
)
Just my two pence on how to do the whole special nature type Kekkei Genkai thing.