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.