Personally, I liked the Zabuza/Haku part of the Intro arc best... because it felt powerful. Well, on the other hand, that's only compared to the "introducing team seven" stuff that was a pretty damn slow way to start the story. (In retrospect, the manga should have started with Team Seven walking out the Main Gate of Konoha, their first real mission as genin; we get introduced to the team for a few chapters, then they confront a villain, then we only see the rest of Konoha once we're anchored to characters that can focus the narrative).
But I think the "Chuunin Exam" was probably the best arc. It was interesting, it introduced a lot of elements and built the world, it just had a lot of novel stuff going on.
Worst arc...
In my opinion, the Kazakage rescue arc. It wasn't all that bad, exactly, it's just that Kishimoto made a huge mistake that he never recovered from: a retired person and a 15-year-old chuunin defeated an Akatsuki member.
He spent the whole series up to that point building them up as the Kingdom of Monsters -- the previous arc villain Orochimaru fled them because he was afraid they'd gank him! -- and he even made Deidara appropriately into someone who really could threaten an entire village with his flying+bombing combo; but then Sasori was just a pile of medium-strength parental issues that lost.
Like, if it had been his old partner (Orochimaru); do you think Orochimaru would have lost to some old bag and Sakura? No, he would have killed Sakura, used the old lady as a sacrifice to bring Sakura back as his Edo Tensei zombie, and then Orochimaru would use zombie!Sakura to fuck with Sasuke and Naruto's heads for a bunch more chapters.
So when Kishimoto had Sasori lose, he threw away the "untouchability" the Akatsuki had for the two hundred chapters until then, and for no real gain; Sasori lost to the "normal" girl and some old lady introduced five chapters earlier and only ever seen in cameos after that.
That got even worse in the Hidan / Kakuuzu arc; Kakuuzu bragged about butting heads with the First Hokage, and he had the best immortality jutsu in the whole series. Standing next to him, Hidan was literally an unkillable servant of an evil god. Maybe there never actually was an "evil god", but the "unkillable" part was pretty heavy-duty, so it was still fine.
And they lost to Shikamaru. Another "normal" guy. Maybe he was kinda smart, but compared to guys that sweat blood and worked 'till they puked every day, like Lee, like Naruto, like Sasuke; he was a chump. Shikamaru was a speedbump, all he could do was use his shadow jutsu to slow people down, he didn't have anything else.
So the thing was, rather than reinforcing the "invincibility" of the Akatsuki by making them literally All the Monsters, Kishimoto threw it all away as soon as he actually used some of them.
He wrote himself into a corner. That's why it was a ridiculous cavalcade of "man behind the man" antics after Invasion of Pein. He had already used up every single villain he'd prepared, so no matter what he did next, it would be too abrupt, it would come from left field.
And rather than having the balls to start up another genuine ninja war....
Well, I feel like that was the same failing we saw with Itachi. Kishimoto didn't have the balls to make Itachi the kind of inscrutable sociopath that would commit genocide "because test my capacity lol", so he had to come up with that absurd "coup" plot twist.
In conclusion, Kishimoto's biggest problem is that he was incapable of having villains win battles.
