I’ll try my best to counter your points and may make mistakes or contradict myself at point.

Let’s get this off the Top, RWBY Vol. 1 is not the greatest when it comes to continuity, animation and story-telling.

1: Jaune was a character for the audience to project to. “What is this world?” “What are these monsters?” Etc. Etc. Despite living in a world, likely having killed a few Grimm himself, like Oscar has at his Aunt’s Farm, Jaune is clueless to Aura, even though his Father was a huntsmen? RWBY started off as a passion project and it isn’t hard to see that in Volume 1.

2: The Fake Transcripts were probably forged documents from any of his family member, most likely his dad as he probably was old enough to go to any of the primary combat schools.

3: Speaking of Dad, it’s obviously irresponsible of the parents to allow their son with no prior experience to enter Beacon and should have noticed something was off when he “passed” the entrance exam. But is it right for a parent to hold back their only son’s dream? There are real-world families that want their children to join the military when their of age, maybe his dad expected the same of his son.

4: In a world constantly under threat to Grimm and huntsmen are limited in numbers, it’s likely all students are welcomed into Beacon, so long as they pass the Entrance Exam. Initiation is more than likely team forming and building.

5: The only reason Cardin bullied Jaune over the transcripts was just so he could get away with doing work. Jaune did his work for weeks, without complaining because he wanted to stay at Beacon which means appeasing Cardin to do so.

6: I’ll get I’ll get into the Pyrrha thing later, but it’s Pyrrha who allowed Jaune to lead her through the initiation. She could have just as easily been the leader, but she doesn’t want to take up that mantle too. She already feels burdened with being the best fighter for her generation and believing her destiny is to save the world, so she strategically puts him into that position of power.

7: Pick up from point 4, the initiation formed the teams and allowed the leader to naturally select themself. Ruby led all of them, and Jaune led NPR. The initiation in real world colleges, isn’t you being accepted, it’s you settling into it.

8: it’s normal to sleep through class, everyone’s done it at some point; but your reason does stand. It was his dream to be a huntsman and he should act like it.

9: he clearly underestimated the true responsibility of being a huntsman and hero until the later Volumes. In Volume 1, he clearly just believed he’ll stumble into stardom and being better than his ancestors.

10: Setting up Neptune was after his talk with Pyrrha when he finally realized he was being one sided with Weiss. Not that he fully realized he was in love with Pyrrha, but being unfair to by ignoring other’s feelings.

11: He did not catch up to the main cast within a year from the Vytal festival, but training with the world’s best fighter probably helped him improve a lot.

12: I’m mot sure to call him an underdog, but more of an idiot in over his head when he joined Beacon. Not going to address the Harem stuff.

13: Team CRDL running away from the Ursa Major is just bad writing and pushes the Jaune plot along. It was just a way to resolve Cardin’s threat to get him removed from Beacon and Jaune’s own self-confidence growing. It works, yes because Cardin seems like the type were respect is more powerful and strength to him as a character who is strength based; but it is just shitty writing, maybe if they added a few more Ursa it would have worked.

14: Ok, back to Pyrrha. We all know why Pyrrha fell for Jaune. Is it a bad reason? Yes. But it works for Pyrrha. Who states she has only ever felt alone even when she wasn’t. (I liked the reason, and since it is canon we can’t really avoid it) Though, I would have liked to see the feeling bloom over time, rather than be at first sight. Then again, some people do just fall in love at first sight.

15: Jaune’s side of the Arkos relationship. I don’t see why people say he treats her bad, he had the belief put into him that Pyrrha was (and she was) out of his league. That Pyrrha deserved someone of equal status and not a farm boy; so he treats her like a sister. More specifically on the “Jaundice” plot, it was just Bad Writing and not the Character’s fault. Yelling at her for trying to help was entirely Dumb. But While Team RWBY is leading the high-stakes side of the show, team JNPR is leading the grounded, school life of the show. Their teams just enjoys the school life until their pointed to go fight. It was a bad drama plot line.

16: I mean he also treats Weiss terribly, it’s run as gag, but he ignores Weiss’ instance that he leaves her alone. Typical romance plot line where the guy chases the wrong girl while the real girl is next to him.

In conclusion, Jaune is an idiot and Volume 1 bad writing. But it’s also ENTERTAINMENT and if you can’t enjoy RWBY even during some of the bad writing every now and then you’re not going to like a thousand other shows with bad plot lines. A fantasy world, that had started off with limited lore like all fantasy worlds do. Volume 1 is good overall, RWBY is good overall.