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About two years ago, when I was still in college, I took a creative writing course as an extra credit. It gave me some insight into the way writers think, and ever since I've developed an eye for picking up on certain patterns. Now I am by no means comparing myself to Tui T. Sutherland, she has WAY more experience publishing books than I do. All my criticisms are being done with the benefit of hindsight, and at this time I am doubtful I could come up with an entirely fleshed out multi-book arc from scratch.
Not long after I graduated I began my Magnum Opus as a hobby, but I got to a point where I realized I hadn't planned that far ahead, and out of a sense of desperation I tried to quickly make a conclusion. I rewrote it over a dozen times, each one feeling more unsatisfactory then the last, and eventually I shelved the project entirely. I bring this anecdote up because I have noticed that when Tui is rushing she'll write by the seat of her pants, and nowhere is this more evident than the second arc. Entire plotlines are replaced by new ones with little foreshadowing, things set up early on don't get proper payoff, and the tone between books become a little inconsistent.
I can't fully blame her though. When you look at the release schedule for the arc, Tui was making on average a three hundred page book every four months! That's a book having to be finished, edited, approved, and built up enough stock for release day. That is insane. Of course some of this process can be overlapped, but I would not be surprised to hear she was bouncing between multiple books at the same time. (By arc three Tui slowed to about a book every year, and while I think that arc has some issues of its own, it's at least more consistent than the second.)
It is my belief that Wings Of Fire was in a position similar to The Legend Of Korra: they had only panned to release the first arc/season, but when the publication company/studio saw the sales/ratings they demanded a part two, and they had to rush to make the deadline, sacrificing quality because of it.
With all that background info addressed, lets get into why I don't believe arc 2's romantic subplots work.
The short answer is a lack of proactivity. Rather than taking an active stance, most protagonists feel like they're just sitting around waiting for the subplot to solve itself. The love triangle feels like it has the three holding their breath to see who messes up first so the other two can get together. Turtlejou feels like the author realized she hadn't given either character a serious love interest and so she slapped them together with a contrived love spell. It's why I love Cleril; a lot of Peril's actions are driven by her feelings for Clay. It's why I consider Winterwatcher well handled despite their poor chemistry; realizing his feelings for Moon plays a big factor in Winter's decision to leave his tribe behind. The romantic subplots in the first half feel very carefully laid out, while the ones in the second half seem to be slapped together because the author says so.
I know I keep coming back to the love triangle, but its poor handling really is the most prominent plot hole to me in the entire arc. While trying to keep as much as the overall plot intact, this is how I would go about rewriting it.
***
Book 10 starts a little earlier than in canon, with Moon telling Qibli and Winter that Darkstalker has offered her to accompany him to the Rainforest. Qibli is concerned but says he'll support whichever decision she makes. Winter on the other hand is appalled that she would choose to leave them and insists she stay. It escalates into a big argument, where Winter begins to really lay into her, some of which is deserved, some of which is not. He blames her for Peril burning Darkstalker's scroll, and also for "making him return to Possibility" where he almost burned to death. In the end he says he should never have left the Ice Kingdom for her, which is when Qibli realizes Winter has feelings for Moon. This is where Moon sets her mind about going with Darkstalker and she and Winter part on bad terms. (This gives Moon an incentive to go with Darkstalker rather than in canon where she just follows him around because the plot demands it. It also gives more time for the drama to stew rather than making it feel like it comes out of left field.)
Now Qibli has a dilemma for part one: he can either try to convince Winter to patch up his relationship with Moon, or he could just not say anything and improve his chances of getting with the girl of his dreams. So while in the Sand Kingdom Qibli tries to get Winter to open up, and slowly over the course of part one he does. It's revealed that Winter has some abandonment issues, which Qibli can relate to. They connect over their troubled childhoods and grow closer as friends. (This solves the biggest problem I have with the Qinter ship, which is a lack of communication.) Eventually Qibli helps Winter come to terms with his complicated feelings, and while he is still annoyed with Moon, Winter agrees he should at least apologize to her for some of the things he said.
Getting into part two it plays out a lot like it does in canon, except the vase scene is replaced with Winter's apology. Moon accepts it, though she's still not quite ready to forgive him entirely. She spends a lot of time with Qibli in this section where feelings begin to blossom. Qibli likes that he's hitting it off with her so well, but feels bad that his two best friends have some amosity between them, so he gives her a few nudges to give Winter a chance, but she's still hesitant. Also, have have Winter reunite with Foeslayer probably offscreen and send her to go talk to Qibli. (As opposed to canon where she just randomly pops up and talks to Qibli when he's alone for little apparent reason.)
Part three again plays out pretty close to the original, but this time Winter declines to fight with the Icewings, choosing instead to stick with his friends. Thus he is not teleported away with the others at the end if the battle. Darkstalker still snatches Qibli away and they have their conversion as normal. Then when they have the final confrontation with Darkstalker Winter is there too, along with Turtle and Peril (whom I have no idea why Tui choose leave those two protagonists out of the scene either. Maybe she has difficulty juggling dialouge between more than five characters at a time? Idk). As much as I don't like the resolution of turning Darkstalker into Peacemaker, I'm gonna leave it in. When it comes to Winter and Peacemaker, he'll agree with the motive but not necessarily the means as it reminds him a little too much about Hailstorm, but he lets it happen for the greater good, showing how far he's come as a character from Book 6.
The Epilouge takes place a couple days later when Moon has asked Qibli and Winter to meet her. She tells Winter she forgives him after he stood with them through to the end. Now the scene is primed for the love triangle to resolve, and we find out which ship is the winner.
Option one: Moon says she appreciates Winter as a friend but her heart goes to Qibli; Winter would be a little bummed out but says it's probably for the best after the way he treated her in the beginning.
Option two: Moon says she's willing to start over with Winter, which would fulfill Qibli's narative goal of getting his two friends back together so it doesn't feel like he gets left out to dry.
Option three: Moon tells them that she's not ready for a relationship yet and suggests they just stay friends; this leaves Qibli and Winter surprised, but they all eventually laugh over the silliness of the drama and grow closer as friends (perhaps even leaving the door open for Qinter down the road. This is my personal favorite ending).
Option four: you can jump the shark and have Moon say she loves them both and they agree to a poly relationship; this one is quite self indulgent and probably not at all realistic, but a shipper can dream...
***
There's a couple more scenarios I can think of, like having the triangle be between Winter, Kinkajou, and Turtle; or having Moon and Kinkajou get together; or even bringing back Umber and his crush on Qibli. But this story I've crafted above is the one I really wanted to get off my chest and the one I'm most content with.