The funny thing is that the problem Kishi had with the series is that he didn't have HunterxHunter to copy from after a point. I like Naruto and am not a fan of HunterxHunter, though it's easy to see what was lifted from HunterxHunter. The thing is that Kishi was able to reimagine those arcs and characters far better. When he ran out of a template to work from though he really began to shit the bed. The real downfall of the series though in my view was still the pain arc in the anime. The manga was fine till Pain brought everyone back to life, and Kishi killed of Konan for no real reason, despite him taking a strong no death stance.
I think it had something to do with the earthquake at the time. A lot of mangaka were changing how they did things. It's also when HSOTD stopped due to all the depressing shit and death in Japan. Studio's I think wanted more escapism rather than being reminded of the death around them. I think that may have also been the trigger for Isekai to become popular. It's like dead people just go to another world and get harems and demon lords to kill, it's fine!