head to head
Neither is meaningfully harder - they pose close to the same test. The widest gap is execution, and it is a single point.

Execution · Competitive PvP
Arena fighting built on baiting substitutions and timing punishes against humans.

Execution · Competitive PvP
Fast anime fights where combo execution and reading a human rival decide rounds.
Naruto Shippuden: Ultimate Ninja Storm 3 leans Execution (Competitive PvP); Naruto: Ultimate Ninja 3 leans Execution (Competitive PvP).
Naruto: Ultimate Ninja 3 leans a little harder on execution, though the gap is small.
Naruto Shippuden: Ultimate Ninja Storm 3
Substitution timing and combo confirms need decent hands
Naruto: Ultimate Ninja 3
Combo timing and jutsu clashes reward quick hands
Same score on reads - which means the number cannot separate them. The difference is in what each one asks of you.
Naruto Shippuden: Ultimate Ninja Storm 3
PvP revolves around baiting substitutions from human opponents
Naruto: Ultimate Ninja 3
Human versus play rewards baiting and habit punishing
Naruto Shippuden: Ultimate Ninja Storm 3 leans a little harder on variance, though the gap is small.
Naruto Shippuden: Ultimate Ninja Storm 3
Support meter and item randomness barely matter
Naruto: Ultimate Ninja 3
Fights are deterministic outside clash minigames
Same score on optimization - which means the number cannot separate them. The difference is in what each one asks of you.
Naruto Shippuden: Ultimate Ninja Storm 3
Team composition and awakening knowledge add a thin layer
Naruto: Ultimate Ninja 3
Character matchups and meter use are a thin learnable layer
A matching score does not mean a matching test. Two games can both sit at 10 on execution and demand completely different things of you - which is why the reasoning above matters more than the number beside it.