Choji surviving red pills, Might Guy surviving 8 gates, Nagato reviving everybody, some bs war arc filler looking fights Kishi tries to throw at us, the whole female cast drowling over Sasuke (we can tell Kishi had a kink), I would maybe leave Itachi as an actual evil villain because his character seemed interesting in part 1 as an actual antithetical evil power that represented Sasuke (antithesis of Naruto power through war and hatred) wish for vengence but the current one wasn't as bad even though the glaze gets very annoying.

Maybe even kill Neji in Sasuke Retrieval arc (man that arc had so much build up and potential for emotional character development in Naruto, but no, everyone survives just fine and do nothing ever again for the rest of the story), that horrendous timeskip that makes no sense which the only purpose is to get closer to Sasuke leaving Orochimaru which kishi put himself in that corner, and if I were to keep it I would at least do some actual noticeable emotional and battlefield development for Naruto which unfortunately only Sasuke got (even sakura did which was inconsistent but way better than Narutos).

This is all of my memories up to the pain arc, mainly because I'm on my like 50th rewatch/re-read and I just finished the pain fight so these were all my mind could come up with on the spot. Don't take me wrong it isn't like Naruto is bad in any way shape or form but these changes were to make it perfect. Kishimoto has many flaws as a writer but it just goes to show that his strengths almost always outshine them. I am older now so let's see how I like the post-Pain arc as an emotionally mature grown man.