It doesn't affect the gameplay in my opinion.

I just see the storyline as a "companion" story to the actual canon - the only difference being that the only competent ANBU (you) is keeping an eye on his/her childhood buddy Naruto.

There are a couple deviations from canon that I've noticed, mostly involving the main character's separate ANBU missions (for example, when you're investigating the forest for disturbances and run into the Sound Genin. Dosu is still alive, while in canon he should've been killed by Gaara at that time).

But it doesn't affect the gameplay, does it?