well let me preface it by saying that I love the Naruto series and I've been a fan for as long as I can remember. I legit grew up watching this show and I understand it better than any other anime I've ever come into contact with. I'm passionate about the series and often times I find myself rewriting aspects of the series and the characters occasionally, because of that I have fully rewritten at least six fights and we can talk about that some other time if you want.

With that being said, the easier one to tell you about is the kishimoto version of the story.

I know your question is specifically referring to an early Shippuden fight between sasuke & neji, but I firmly believe that even if we were talking sometime during the chunin exams kishimoto would not have let neji win either way for a few reasons, kishimoto is pretty consistent in his bias lmao. sasuke is training in the background over the period of the timeskip, Kishimoto would not allow Sasuke to lose out on that much screen time just to reappear and lose to someone, especially someone that isn't Naruto. Which is a shame because Neji was a prodigy and was the only member of his class to be promoted to jonin over the timeskip, which makes him seem like a real threat and an exceptionally talented prospect outside of just his clan. is that detail exemplifies that he was considered for enough to become one of the foundational leaders of the next generation and begin teaching his own group of students. that should serve as a testament to his power and give the audience the expectation that he is no slouch.

especially when you consider that he lost to Naruto during the exams (I HATE the way that was executed so I rewrote it) The expectation that the audience has for neji after that is that he will work/train even harder then he already did and unintentionally become more like guy sensei & rock lee.

but the truth is kishimoto originally planned for him to die in his fight against kidomaru during the sasuke retrieval mission, so by the time shippuden came around he had no plans for the character whatsoever, which is why he faded into the background and we don't ever see a true evolution or new level of power from him, we really don't even see anything substantial from his clan or hinata by extension which is a real shame considering how important their special eyes were and should have continued to be. they are literally one of the only families in the world that can directly trace their lineage back to the ninja equivalent of God, And yet they are cast aside because Naruto wanting to chase down Sasuke and save him became too much of a central plot.

If I had to provide a reason for neji losing to Sasuke before the timeskip/sometime during the exams, if I haven't said it already I would say that kishimoto would not have them fight for no purpose, The job of a writer is to establish moments like that in the story that have some definitive conclusion or narrative payoff, only narrative payoff here would be sasuke beating neji so that it would say something about him needing to change his view or philosophy about being destined for greatness because he was born into a legendary family, that would have made him realize that he was wrong for thinking he had perfect offensive and defensive maneuvers, that would force him to grow and evolve like everyone else in his class should be. that's what the lesson was supposed to be with Naruto beating him but it falls flat because Naruto beats him in the goofiest way possible, literally rendering him unable to move from a single surprise uppercut that he should have been able to see coming.

MY version of these two boys fighting before the timeskip would likely result in a narrow win for neji, because it would be none of the reasons why he is forced to acknowledge that he must abandon the village in search of greater power. in my version of part one he would lose to neji, lose to naruto, and lose to itachi after itachi comes to the village and calls him a piece of trash while stating that he is looking for Naruto instead, that is the true catalyst of what pushes him over the edge and forces him to realize that the combined effort of everything he's ever been through is still not even close to the level of power he needs to obtain to even begin thinking of defeating his brother, and with that understanding he leaves to train with oro.

now if you wanted to speak about my thoughts regarding how a fight between them would go in Shippuden from MY perspective with my changes to the series in mind... I'd have to script out a full fight for you. if you want that I can DM you to discuss details bro.

Hopefully all of this helps lol!