Probably clear time is taken into account too, for example it took you longer than him because your shisui did 1000 attacks and he used faster lineup

Hello,
Nature training changed as of last month. In addition to the previous methods for obtaining points and ranking, bonus points are given out for using ninjas of the correct elements. The reason your rival has a higher score than you is likely because he used ninjas of the corresponding antagonist element.
Thanks and have a great day!

Hello,

In the current state of Nature Training the things taken into account for the point system are indeed the time (rounds) needed to clear and the use of the right counter ninja. the more counter ninja you use the higher your score can become.

The last update to nature training was mid-July:

1. Update to Nature Training: All element Trainings will have completely new set ups
2. Use the correct counter-element ninjas for an element Training to get extra points in the rankings, for each correct counter-element ninja, players will get extra points
3. The amount of extra points given is decided based on the Level of the training players are doing
4. For example: Level 25 will give 7 extra points for every correct counter-element ninja
5. Level 50 will give 15 extra points for every correct counter-element ninja
   

I did not hope for such complete info but here it is...Thank you so so much <3