Well, first off you must be a crazy spender to even be asking this question unless your playing theorycraft...

From worst to best (imo)
1) Standard attack. Increase his combo rate.
2) Infinite Darkness passive. You can make him blind 1 random ninja every turn, blind 2 ninjas every turn for an additional frag cost (unknown how many)
3) Ninja God passive. CHANGE from 30% taijutsu to 15% critical rate to entire formation.

These are all ridiculously expensive for a ninja that is mediocre at best even in a great team. I say the Ninja God passive is the only one worth looking at because critical rate is very impactful to any ninja in a 12 man formation.

The only upgrade that isn't RNG is the ninja god buff. It's up to you of course.