Just playing around with Naruto's development. It bug me long time.
Naruto doesn't learn the Shadow Clone Jutsu before Iruka arrives despite his hard work. It's only when Iruka's in danger that he pulls it off, starting the theme of protecting others being the path to true strength and giving an excuse for mastering a B-rank when he struggles with E-ranks. Early on, his clones dispel after one good hit and the numbers he creates are inconsistent but these problems resolve over time as his skill improves.
Genin are shown to have a more regular intake of D-rank and C-rank missions, undergo coordinated training as teams and use some new jutsu such as the Temporary Paralysis and Body Flicker. Just to emphasize that they have been learning things during their time as a genin than aren't limited to their clan jutsu, and that teams do end up spending a lot of time together.
Each time Naruto fights with his shadow clones, he would have unconscious flashes of insight from the jutsu's memory recall but not being particularly introspective, he wouldn't put much thought into it outside of the battle. For instance, after dispelling all of his clones in the genin test he intuitively knows where Kakashi had substituted himself to or, like Sasuke, grew better able to grasp Haku's movements between the mirrors from their shared experience. Just not enough to save him.
Instead of Zori and Waraji, Zabuza sends
three genin subordinates to kidnap Tsunami/Inari. Just as Sasuke got to show off the fruits of his training against Zabuza's clones and Haku, Naruto shows off his own growth by defeating these three himself with surprise, shadow clones and chakra enhancement. Zori and Waraji are in the crowd that accompany Gatou to the bridge and get killed by Zabuza.
Possibly Kakashi teaches Team 7 the water walking exercise between the Land of Waves and the Chuunin Exams. It'd show that he continued to teach them, would make them better prepared for the exam and show them working as a team again. They'd only learn the very basics and Naruto would continue the training with Ebisu later.
In the Forest of Death, Naruto isn't separated from the team by Orochimaru and gets caught in the same terrifying experience as Sasuke and Sakura, so his willingess to fight back against Orochimaru looks less like ignorance of the danger and more like genuine courage. He's still knocked unconscious but wakes up in time to bear witness to Sasuke's curse seal. That way Naruto isn't ignorant of the important plot-related events and has some understanding of what's happening with his teammate, even if there's nothing he can actually do about it.
In the preliminaries, Naruto creates shadow clones to block Kiba before he can attack him and then launche the Naruto Combo, granting him victory. Nothing more, nothing less. -_-
Kakashi/Jiraiya clearly explain the memory recall function Naruto had discovered and while he's practising water walking and the Summoning Jutsu, he starts to take advantage of it. He uses them to come up with different maneuvers and tactics to deal with Neji and practice them in his place. So Naruto is able to accumulate the experience of that practice without being distracted from his main training. It highlights the "Heaven and Earth" motto that chuunin are meant to live up so Naruto is showing some actual forethought.
Jiraiya considers it surprisingly ingenious. No-one had thought of using shadow clones for training before. The closest thing to it is when a shadow clone acquires useful knowledge in the ninja's place such as from reading a scroll. Naruto puts on a better show against Neji in the first half of the fight but it still comes down his chakra points being blocked and using the Kyuubi's chakra to gain victory.
[Insert Naruto vs Kimimaro tweak here]
Naruto spent the timeskip taking missions with Jiraiya for training and to earn money instead of just travelling. His training had taught him to use the Rasengan one-handed and to create shadow clones with just the seal of confrontation and/or no hand-seals.
When Naruto's caught in Itachi's genjutsu, he remembers what
Kakashi taught him and the rest of Team 7 about breaking genjutsu and successfully escapes it. Another example of the genin clearly learning skills from their jounins in Part 1 and better demonstrating Naruto's growth considering he kept getting caught in them before.
Kakashi tells Naruto about the Fourth Hokage's idea to create an elemental Rasengan. To create this seemingly impossible jutsu, the shadow clone training method is devised. Either Kakashi comes up with the idea based on what Jiraiya had told him about Naruto's training method or Naruto himself comes up with it before or during training, inspired by his motivation to surpass Sasuke.
[Insert Rasenshuriken/Senjutsu training tweak here]
Or something like this from one of my old posts: Naruto returns from the training trip having mastered wind nature transformation and the Rasengan. He's been trying to use the Wind Release Rasengan one-handed but the jutsu has several issues; it's hard to sustain, unstable and tears his arm up every time he uses it. He'd use it to kill the fake Itachi instead of the Big Ball Rasengan. After the Sasuke and Sasuke Arc, he works on perfecting it and after numerous failures, he realizes that instead of obstinately doing things alone (like Sasuke) he needs to get back to basics. So he whips out a shadow clone to share the load and hey ho, he's finally created the Wind Release Rasenshuriken. Which he later throws in Kakuzu's face.
Might be pushing things with that version though.
Anyway, Naruto's perfect mastery of senjutsu would be the result of Jiraiya teaching Naruto meditation during the timeskip to grant him better control of his chakra and emotions, his body being naturally adept at handling foreign energy because of the constant influx of the Kyuubi's chakra and the fact that he just seriously
worked his ass off for a more believable length of time.
And there'd be glimpses of Naruto continuing to use shadow clones for training such as improving chakra control, perfecting his jutsu, maybe mastering other chakra natures for alternate Rasengans, shortening his Sage Mode's activation speed and lengthening its duration. It wouldn't have a huge impact overall but it'd show that the training method isn't being ignored after the Hidan and Kakuzu Arc.
I feel like I should come up with something about his chakra modes and whatnot...oh well. This post is big enough as is.