Well yeah, that is price that you pay for when you, 1) create a Shonen manga in which the focus is placed on bigger stakes rather than dynamic characters, and 2) fail to create a plot outline, or at bare minimum have an idea where the story is headed before you put ink to paper.
Don't get me wrong, I have eternal respect for Kishimoto and I will always cherish and love Naruto despite its many flaws. When Kishimoto started this crazy party 2 decades ago with his original manga pilot, he very obviously had a different manga in mind before he eventually chiseled out the Naruto we all know today. It's also practically common knowledge that if it weren't for his editors in the beginning, we wouldn't have characters like Sasuke or Sakura—say what you want about that, but I take that as confirmation that Kishimoto either had absolutely no plan for the manga to begin with or again, had something different in mind before he worked out what he have today through editorial feedback. Part 1 is so fundamentally underrated by people, which is a shame because that's where the series highest points are and if Kishimoto essentially pulled each arc out of his ass as he went/received feedback during Part 1 then I truly do commend him for his phenomenal work.
However by the time Kishimoto started Part 2, the training wheels needed to come off. By then he had (ball-parking) 200~ chapters under his belt, built a solid foundation for where the main plot needed to go as well as set the stage for other plotlines as well. I can believe that Kishimoto planned ahead a basic story outline from Part 2's start all the way up to Naruto and Sasuke's reunion at Orochimaru's hideout... maybe he had something for Hidan and Kakuzu as well but I don't know if I'd believe even that. But planning out Jiraya vs Pain and the intricacies of their background? Tobi? The first major plot twist in the series where Itachi was actually a good guy? Naruto vs Pain? Nah, I really just don't believe he had those planned out until he needed to start planning them out. It becomes apparent that there was a severe lack of planning more and more as the series goes on beyond the Pain invasion arc leading up to the granddaddy of all that is legendary, while at the same time horribly disappointing, the War arc and conclusion.
I'm not saying a mangeka needs to have their entire story mapped out prior to Chapter 1, but there is a moment in all long-running manga where it becomes clear how much homework the mangeka did in advance and how that prep work (or lack thereof) will affect the manga going forward. They are at the end of the day story tellers, and as such have a responsibility to their audiences not to BS it as they go along. In my opinion, that "moment" in Naruto was Chapter 490—when Kabuto summons the 6th casket with a mystery character within. Now first, those were the REAL days of Naruto base because that's when we'd get super creative and interesting theories and discussions on these mysteries of Naruto... BUT if you look back at that chapter with what we know now, it makes absolutely no sense in any manor. How did Kabuto find Madara's body if it's safe keeping was (presumably) left to Obito and Zetsu? What was Obito freaking out about? Since Madara was able to break free of Edo Tensei later on, Obito should have some idea that Madara is just that gud and should have been thanking Kabuto for making his job INFINITELY easier. It was a great setup/mystery, but I just don't think even Kishimoto knew what was in it until he could come up with something convenient and the same was likely true for Tobi's identity for a long time as well.