You're not alone here, lots of people found Cytonic to be the worst of the series. I thought it was fine, but definitely weaker than the others for me, on par with Sunreach and ReDawn. Evershore, meanwhile, is my favorite work in the series tied with Defiant.
Oh, I high-key disagree on nearly every point, though it's been a year or so since I read Evershore. Jorgen is fighting with Spensa for my favorite character of the series so far, I find him super relatable and definitely boyfriend material if he was real.
He was interesting from the first book - not perfect, sure, but far from a villain; he was an antagonist only because Spensa chose him as one. She antagonized him first. He had privilege that he didn't necessarily deserve, but he worked to earn it and clearly cared about his flight, even as Spensa continually harassed him. To be clear, I find Spensa also incredibly relatable, especially early on! I want her to succeed! But Skyward is supposed to show that her fiery approach to the world can't be applied unilaterally. She and Jorgen did better when they worked together, and when Spensa reached out, Jorgen did the same. He wasn't being "redeemed" to be the love interest: he and Spensa were growing as people, together, and learning more about each other, and letting each other in. There was no redemption because there was never one necessary (unlike Ironsides, who debatably got a last-minute redemption?).
When reading Starsight, I also was a bit surprised that Jorgen was cytonic, and did figure Brandon had done it because he was the book one love interest (Janci wasn't involved in the writing until the novellas). I understood it more as we learned that different cytonics specialize in different abilities, though - you need more than one character to display all the cool powers so that no individual is too OP, so of course the main cast would have more than one cytonic in it.
I checked out chapter 14 and genuinely have no idea where you're seeing any of that, except I guess him not inspiring confidence? Which I think is kind of the point, they're all in a bad position during Evershore and nobody's confident! Their only leaders are terrible at their jobs, and Jorgen has to step up because he's one of the only people with actual experience who will do the right thing. Yeah he's young because it's YA, but with the situation the way it is, he's one of the best people they've got - ideally he wouldn't have to fight at all at his age, but he does; they do. Of the available characters, he has far better leadership skills than Stoff or the nameless admins. Cobb is probably better, but Cobb wasn't able to do it anymore.
I think calling what he does whining is a pretty ungenerous reading of the situation - the dude's got PTSD on top of PTSD, what with them all being active soldiers at a young age and then losing his parents in front of him. I found the symptoms to be clear and well-written, and my heart went out to him throughout the book. He argued with FM (which was a growth moment for both their arcs), but that doesn't mean he was 100% wrong in all his choices.
As someone who also appreciates structure and rules and knowing what to do, I really love Jorgen and the way he thinks about things. Who he is is a strength in the end, and I could not disagree more that he is boring or annoying. It's valid for you to like or dislike any character or to be bored or annoyed by them, but yeah, I don't see anything you're saying here myself.