I got a couple ideas from others in this thread that changed my mind so disclamer: these ideas aren't all mine, it's just my own personal combo, mix and matched ideas of others and my own that I thnk would have made the manga better.
Power levels and techniques:
- Make genjutsu more visually appealing, creating a wider variety and generally make it more exciting, aswell as making it a more significant part of the manga rather than restricting it because of it's OPness. Conversely, make genjutsu more counter-able through techniques/jutsu rather than just forcibly charging your chakra, PARTICULARLY make sharingan genjutsu more counter-able, too OP.
- Show more love to other chakra natures rather than just Raiton which seems to have the highest number of sick techniques. I'm not talking about quantity I'm talking about quality, I think Suiton has the most techs but only a few are actually awesome. Same goes for the rest of the chakra natures.
- More explanation behind Byakugan and it's lineage.
- More explanation and more information on character's chakra natures, base chakra levels/overall chakra levels, SHUNSHIN, foot speed and body movement speed WITH CONSISTENCY. Shunshin was never explicitly explained and for something that was introduced so early and seemed so impressive it seemed a little odd it was never explained, caused a lot of confusion for me early on when I would see Kakashi move so fast one moment but not the next. Also this info provided in the manga would have been a god send for Naruto Base.
-Have more powerful KKG other than chakra natures or dojutsu. Highlight the power of chakra nature combination KKG and have users with better mastery over it, similar to Hashirama and wood style. Not as powerful of course but some impressive mastery all the same.
Characters and plot:
-Ten-ten has more development aswell as Shino and Kiba. Ten-ten becomes specialised in her own unique kind of weapon becoming extremely skilled in it and beoming far more powerful while using it, escaping her mediocrity and no longer being seen as "convenient" (which is filler but still so true).
- We witness prime Hiruzen in atleast one fight.
- We see Kakashi use a larger portion of his "1000 jutsu" and we see him copy other's jutsu throughout the manga since that was the angle Kishi was originally taking with Kakashi in the first place.
-After Sakura and Naruto find Sasuke and Sasuke is still far stronger than both of them, Sakura decides to hit the training fields to improve her taijutsu and physical capabilities. There, she meets Rock Lee, and together they train and develop a strong bond, not romantic but close friendship with a few little hints. After the Kage summit she loses all ROMANTIC but not friendship feelings towards Sasuke. Later in the manga she ends up with Rock Lee.
-We find out Sakura is storing her byakugou seal with chakra much earlier in the story.
- Naruto vs Kakuzu, Kakuzu pushes Naruto and the rest of the squad to their absolute limits, but Naruto manages to get off one successful Rasen Shuriken after MUCH effort and rigour. The fight is extensive even after Naruto arrives and even then it is difficult.
- During the Pain arc, Nagato destroys the village then Naruto defeats the paths of Pain in the same way. Nagato and him have the same talk but Nagato tells him he only has enough chakra left to save one person and tells Naruto to choose. Naruto obviously says he can't possibly choose and so Nagato chooses for him, choosing Kakashi to stay alive as he was a the next most formidable opponent to him behind Naruto and could deem very useful to the village/Naruto and his goal. Many, many, many people die and the village is left in ruins of course. Choji's father dies which brings more meaning and a new level of seriousness to Choji. Fukusaku dies, leaving Shima widowed.
- Post Pain War arc, Naruto realises his weakness in letting those close to him die/get injured (Fukusaku, Hinata, Boss Toads) and continues to strive towards becoming more powerful without reliance on the Kyuubi's power, which he realises happened once again against the Six Paths of Pain and his drive to become stronger becomes even more profound as Minato tells him about the new more powerful enemy. He goes back to Mount Myoboku and starts training with Shima who wants to carry on her beloved Fukasaku and Jiraiya's will by training Naruto. She trains him in Fuuton techniques and teaches him his only genjutsu technique, Frog Song, which he first replicates with her than replicates with his kage bunshins therefore only needing two kage bunshins or one kage bunshin + himself to perform it. He works hard at improving his body strength, speed and overall physical performance aswell as his taijutsu. He also continues to master Sage Mode/nature energy by improving his duration of it and number of clones he can have gather nature energy at once. In general he improves his overall ability as a ninja and eliminates some of his weaknesses which increases his versatility.
- During the war arc, when Naruto is undergoing his Bijuu training, he still defeats Kurama with the help of Kushina but after considering alot of what Gyuki said he was like as a bijuu before meeting Bee and having flashbacks from Sasuke's hatred, he says sorry to the Kyuubi and chooses not to use Kurama's power despite obtaining it because he recognises the Kyuubi as a living being with a soul and conscience thats not a weapon, and that the Kyuubi is just consumed by hatred much like Sasuke. This is the first and very pivotal moment in their relationship and Kurama has his Hagoromo flashback. Kurama not too long after, asks him why he chose not to use his power and Naruto tells him why, Kurama is shocked by this and so then proceeds to open up to Naruto, telling him his name and his story creating a truce between the two.
- Obito manipulates the other villages and pits them against eachother starting a war between the villages with the Leaf and Sand as allies, Danzo's actions contribute to the conflict. While they are fighting the Akatsuki makes it's move against the villages with their white zetsu army and edo tensei pawns. The villages later realise after considerabe bloodshed that they have to collaborate to defeat the Akatsuki. The war is much more punishing on the emotions and feelings of K11 and other key characters.
- Naruto continues to refuse Kurama's power in the war arc up until the 5 Kage vs Madara fight. Kurama forcibly gives Naruto his chakra to help fight against Madara and stop him in his tracks because Kurama deeply fears Madara. From then on Naruto uses BM until Kurama get's extracted. Kurama get's extracted from Minato aswell. Obito manages to get off his rinne rebirth technique before BZ can stop him and Obito saves Naruto's life however Kurama remains removed from Naruto. Naruto and Sasuke have their meeting with Sage of Six Paths and Naruto receives his regular Rikudou Sage Mode however actually receives universal understanding of chakra and as a result is able to essentially pull new jutsu out of his ass with only a small amount of effort and does so throughout the rest of the war arc. Sasuke receives the same thing, the rinnegan but this time the SO6P imparts all his knowledge of the Rinnegan with Sasuke and being the genius Sasuke is, he readily learnt but not completely mastered, every rinnegan path and technique under the sun.
- Neji's death has far more impact on his team. Ten-ten is far more shaken up as is Lee. Lee's demeanor changes from cool, calm and collected to flat out furious and extremely frustrated as his #1 rival has just died.
- Naruto + Sasuke vs Juubidara, Madara kills Guy before Naruto arrives and this pushes Lee to go full apeshit and through sheer will power, he opens his 7th gate and continues going head to head against Madara but alas Madara still wrecks Lee and the same situation takes place where Naruto flys in at the last moment to save Lee from the TSB flying at his incapacitated body. Madara doesn't get fricken nerfed and goes ALL out against Naruto and Sasuke showing much more mastery of the rinnegan and Juubi power.
- BZ still wrecks Madara, Kaguya is resurrected, Kaguya isn't a complete dumbass and seems much more experienced in battle, pushes Naruto, Sasuke, Sakura and Kakashi to their absolute limits. Kakashi gets Obito's transmigrant Sharingan, Sakura doesn't punch Kaguya in the head and another more realistic example portraying team 7's teamwork replaces it.
- Naruto vs Sasuke is perfect except for Sasuke has Rinnegan mastery and Naruto who finally has a plethora/variety of jutsu that he was robbed from receiving in the entire manga unlike Sasuke.
- All bijuu go home except Kurama, who chooses to live near the hidden leaf to help protect it and be near his dear friend Naruto's side.
- Sasuke ends up with Karin and actually returns home to her every once and a while as her husband. Sakura ends up with Lee. Choji doesn't end up with Karui, anyone but her.
- Shin Uchiha isn't covered in sharingan and has a new different power up instead.
