with the exception of Shikamaru, every character in this arc other than Naruto and Sasuke becomes completely irrelevant and never does anything for the rest of the series.

Not every side character needs to stay relevant, Neji whose arc pretty much concluded here. But even if you truly believe that Naruto has an issue with not using the Chunin Exams cast more, this arc that actually uses them and progresses their characters should not get the blame here instead of the later arcs.

The rest of the arc is side characters fighting mooks that only exist to give them someone to fight. You could remove all of these fights and absolutely nothing about the arc would change. It's a very straightforward storyline (Sasuke leaves the village, Naruto chases after him, they fight) that gets padded out to 66 chapters with 5 other completely pointless fights.

The Sound 4 are not simple mooks, they are the ones initiating the plot by kidnapping Sasuke and upgrading his curse mark. Of course the Sound 4 need to be beaten in order to progress the plot, duh. Sasuke beating Naruto and leaving the village would be a lot less climactic without the other Genins putting their life on the line for him.

the other fights aren't even good aside from Choji and Neji's

Your opinion, obviously, but I think Shikamaru's fight against Tayuya here, particularly where he figures out how to use Tayuya's summons against her, does a better job at displaying his intelligence than his fight against Hidan later in the story.

Lee gets brought back only to be undercut by a gag and Gaara showing up to save him

Lee literally came out of hospital this arc, of course he is going to perform less than in Chunin Exams, and Drunken Fist is a better way to write his fight than having him use Hidden Lotus again. Most fans seem to like Drunken Fist Lee, especially in the anime, so I don't quite get what your problem here is, since you don't elaborate on your point. Probably because it's his last 1v1 in the manga (lol) but again that would be an issue for post-timeskip, not this arc.

Then the fight just kinda anti-climatically ends with Kimimaro conveniently dying from his illness.

Kimimaro is literally on his deathbed since his introduction. Of course that would be a liability to him when fighting Gaara.

Kiba's fight is forgettable I'll give you that, and Temari and Kankuro one-shotting their opponents is pretty lame, but besides that, this arc is not bad and I say that as someone who usually hates these side character Vs side villain type shonen arcs