Priority System is definitely easier to grasp for normal attacks, but for Ninjutsu, I stick to a strict rotation:

Huton -> Suiton/Kass Raiton -> Raiton -> Huton -> Suiton -> Raiton, repeat.

Huton is 70s, which allows two other ninjutsu(20s CD) to be cast before you need to reapply, with a narrow 10s of grace. Kassatsu has a 2min CD, which means it should be used on every other Trick Attack. So long as ninjutsus are used at every CD, you will be able to fit in a rotation of 3(+1 for Kass).