They did the same thing with Naruto Uzumaki Chronicles, allow me to prove my point. By the time it was released in the US, Japan was already in the "Rescue Sasuke Arc" and these were changed from the Japanese:
1. The Hokages Chair is empty, in the Japanese Tsunade was sat here.
2. Shikamaru has been demoted to Genin from Chuunin.
3. The Rasengan has been renamed Power Strike.
4. The Kisame boss was replaced with Kabuto.
5. The Evil Clone (Itachi) boss fight was removed.
6. The original game's storyline was changed to remove references to Itachi, Kisame, and Tsunade.
7. All FMV scenes invloving Tsunade, Itachi, and Kisame were removed from the game.
8. Gaara is in his pre-Sasuke arc clothes.
9. The battle with Shukaku Gaara was removed.
What do you expect, the game was released before the dub even reached the Chunin Finals. It can't be helped. It seems as though the game was originally made to be uncut, ,but changed towards the end of productionm as Neji references the time that "You beat me" even though Naruto had not beat him yet, and Maile(Naruto's VA) said she recorded "Rasengan" for the game, even though it was only said in cutscenes in the original, and changed to Powerstrike in the Dub version
*And did you* just copy that from Wikipedia? Their list is missing alot of things, including Kakashi replacing Gaara in the last level, as well as the last boss fight.
I am still waiting for an uncut re-release. Months after it was released, many sites had new pics involving cutscenes cut from the dub version*
It would be nice if they took them out because i don't want to see them but in the japanes show they put them in so the manga could get ahead of the show and right now the show is ahead of the manga.
Fillers exist because the anime is an adaption of the manga
If the anime surpasses he manga, the anime has no souce material to go on. Though at the current Shippuden Pace, Naruto could have skipped the filler and still been good enough to not surpass the manga