Impressive thread. You've made quite a few interesting points, and for the most part you have a compelling argument, so +Rep. However, as you also correctly pointed out, the biggest advantage Sasuke currently has against Neji is character development. If you were comparing Part I Sasuke and Neji, this would be a flawless argument, as even Kakashi pointed out that Sasuke would be no match for him. It's a bit tougher to prove your theory in Part II though, mainly because their entire battle (if it were to be in Neji's favor), depends solely on Neji being able to get into close enough contact with Sasuke to disable his Chakra Network with his Gentle Fist Style. Here are a few counter-arguments to The Hidden Shinobi's Back Up Points:
Genjutsu:
While Neji is certainly more than smart enough to avert his gaze from looking directly into Sasuke's Sharingan, genjutsu actually wouldn't be necessary for Sasuke to use in the first place. Due to the Sharingan's amazing clarity of perception, if the match were to start at close range, or if Neji was able to get close enough to hit Sasuke with Gentle Fist, it's more than likely that he could miss; due to the predictive abilities of the Sharingan, Sasuke would see Neji's strikes before he'd make them, giving him time to block/dodge the hits, just as he was able to read Naruto's movements during their battle at the Valley of the End in Part I; the only thing he wasn't able to completely predict was the Fox Shroud, which Neji lacks. So in terms of One-On-One Taijutsu, Sasuke does have a small advantage, courtesy of his Kekkai Genkai. The same would also apply for Neji's long range techniques, since again, Sasuke would see it before it happened.
Amaterasu:
Neji may have the ability to see chakra being built up for Amaterasu, but that doesn't mean he knows precisely where it'll hit/strike. I'm sure you've noticed that A didn't teleport before he saw Amaterasu, but rather after he confirmed with his eyes where Sasuke was directing it (i.e. his face). In a similar vein, the Chakra being built up could be used for almost any jutsu, Neji would have no way of knowing exactly what it'd be, though he'd most likely assume it'd be a Fire or Lighting Release Technique, and that slip-up could potentially cost him the match.
Susano'o:
From what I gathered, the focal point of Neji getting around Susano'o is merely forcing Sasuke to exert all of his chakra and stamina, and then go on an all-out offensive once he's reached exhaustion. However, we're dealing with 2 extremely strategic shinobi here, and either of them would figure out such a simple strategy the instant they see it in motion. Furthermore, it would be wise to realize that Sasuke does possess a rather large chakra reserve; much greater than Neji's, I'd assume. And with Neji consistently on the defensive, using Rotation to counter Susano'o's constant barrage of attacks, his chakra will suffer substantially as well. Hiding is futile, since the Sharingan can distinguish and assess chakra, as Sasuke pointed out in his battle with Deidara. It also gives Sasuke the upper hand since he'd be able to tell when Neji starts running out of stamina. From an offensive standpoint, Neji is again at a disadvantage; Kakashi and Danzo could only evade Susano'o's arrows due to Kamui and Izanagi; simply 'dodging' the arrows is impossible, or at least highly unlikely, or they would've done so instead of using such chakra-taxing techniques.
To sum things up, the lack of Character Development is truly what hurts Neji's chances in the long run - Sasuke outmatches him in chakra reserves. techniques (power-wise), & speed, important elements in battle that Neji has only shown modest increases in (At least from what I've seen/read in the Anime/Manga). In Part I, Neji definitely would've dominated - but as of now, I'd have to say Sasuke takes this match [Mid-Difficulty].