I think Naruto would seriously benefit from a "Kai" series. It seems like for every 30 seconds of fighting there's 2 minutes of other characters reacting and having flashbacks. If they cut all of that out plus the filler I'd be more than happy to rewatch the original series.
One part in Naruto that really frustrated me was when they were doing some espianoge stuff, Musashi Kishimoto had me invested until the rapping ninja popped up to add unneeded comedy. I swear, Kishimoto has poor writing skills and is probably only in business due to his art and a good editor.
I haven't touched the manga in a few years, so I don't know about that. I'm assuming that only the show has these problems to kill time and add filler so that the show doesn't run past where the manga is.