I brought along my copy of Naruto: Shinobi Retsuden to a press meeting where Naruto: Ninja Destiny was going to be shown to run some tests. With button pressing help from Ludwig Kietzmann over at Joystiq, it's clear that the frame rate has improved. The kunai ghosting effect is gone and sidesteps are more fluid.
Interstingly, the US build takes an extra second or two to load over the Japanese version. The graphics also look different, the US version feels more cel-shaded. Also the US build is considered to be the best version of Naruto: Ninja Destiny. The development team had an extra month of time to work on it, which may explain the "European Version" subtile on the European edition.
Unfortunately the Sannin were locked so I couldn't try them out. On the plus side I was able to confirm their super moves. Orochimaru has the Serpent Sword jutsu, Tsunade has the monstrous strength kick and Jiraiya has the toad fire blast.