Which “themes” are you referring to when you say this? I think most people misunderstand what George RR Martin was actually doing.
If you think the show/book is all about twists and shocking moments that defy expectations, you’re misinterpreting what makes this creative endeavor unique.
Subverting the trope of good intentions and ideals winning out; the noble hero triumphing; good vs evil; etc etc.
Generally the story of GoT so far has favored shrewd schemers who are willing to sacrifice their ideals in favor of recognizing reality.
The last couple of seasons it's kind of gone away from that. But early on the show was notable for how people who believed that right was on their side, who in an ordinary fantasy story would find a way to prevail in the end, met an unexpected and undignified death. Whereas people willing to sacrifice their principles in favor of practicalities have managed to survive.
The dragon queen and the noble heir to the throne ending up on top at the end would seem much more in line with a traditional fantasy story, as opposed to a story that likes to subvert those kinds of expectations.
Indeed, Jon is now the classic fantasy protagonist. He thought he was an illegitimate by-blow but actually he's a prince! He came back from the dead! He's literally the resurrected savior.
I would be surprised if he ended up making it to the end. Seems more likely that he was brought back from the dead so that he could die again, later, in a more meaningful sacrifice.
I think that's a standard interpretation of Game of Thrones... and perhaps it's right, but I've never felt it was accurate.
To me, this series has always been about telling a conventional "heroes journey" fantasy story, but using a unique style of storytelling
from multiple perspectives that magnifies secondary characters and masks the conventional arc.
The best way I can explain this is to imagine telling the original Star Wars trilogy over the course of 8 Game of Thrones style seasons.
Both stories are essentially a "heroes journey" about an unknown adopted nobody (Luke and Jon Snow). The difference is that instead of purely focusing on Luke/Jon the entire time, Game of Thrones heightens the roles of everyone else.
So imagine if Season 1 of "Star Wars" opens with the Organa family on Alderaan. You assume Bail Organa, the patriarch of the family, is the main character of the series. Maybe the show casts some big-name actor to play him. We meet him, his wife, his daughter Leia, various characters in his life, etc.
Meanwhile, we shift focus to a young Imperial Academy recruit named Biggs Darklighter. We meet his family. Maybe he has a girl he leaves behind. He's got an envious buddy named Luke from back home who we briefly meet.
There's other characters we focus on like Admiral Ackbar and his crew. The mysterious hermit named Ben. We spend a lot of time seeing the big baddie of the series, Wilhuff Tarkin do all sorts of terrible things to make us hate him. They'd all be given the same storytelling weight. They'd all be "main characters".
In classic "Game of Thrones" style storytelling, we'd assume Biggs Darklighter was one of the heroes of the story. Him defecting to the Rebel Alliance would be a massive plot point as we watched him rise up the ranks. Meanwhile, we'd assume Bail Organa was the star of the show. His storyline would heat up when his daughter Leia is kidnapped. We'd spend a lot of time dealing with the political intrigue of Alderaan and the fallout of his daughter's kidnap.
Of course, this would all culminate in the very shocking moment in which the entire planet of Alderaan - Bail Organa included, gets completely blown up by a Death Star. Think of the Red Wedding, but magnify it by millions of voices crying out in terror. Imagine how people would freak out as not only is the main star of the show eviscerated, but everyone near and dear to him that we've grown to love are also blasted into star dust.
It would come as a great shock when the pretty boy star of the show Biggs Darklighter is killed in combat by the shadowy figure who is second in command to Tarkin (Vader).
As the show progressed, we'd learn more about the "magic" and mysticism underlying the political drama. We'd learn that there's more to this shadowy Vader character than we believed.
Meanwhile, we follow the young farmboy Luke as he begins his journey.
Other key characters would be introduced along the way.
Following the Game of Thrones model, Luke probably doesn't even find out that he's the son of Darth Vader until Season 8 Episode 1. By then, we'd have seen so much death and destruction that people would assume the show-runners were sadists that had no intention of having a happy ending.
To me, this story has always been about Jon Snow's arc in the same way the original Star Wars is about Luke Skywalker.
Everything in this story feels like it adds context to Jon Snow's story.
- The Starks: Gives context to Jon's moral upbringing and crucial half of his family story
- Kings Landing: Gives context to the throne that belongs to Jon
- The Wall: Gives context to Jon's growth as a leader
- Dany: Her entire arc serves the purpose of giving us context to Jon's Targaryen background while subsequently introducing dragons
I feel like "Game of Thrones" is subversive, but not in the way people think. It's not about defying basic storytelling principles when it comes to the large arc. It's about how much depth and importance is given to the peripheral. Standard storytelling, you tell a story about Alexander the Great completely focused on Alexander the Great from start to finish. In this style, you tell a story about 330s BC Macedon told through the real-time perspective of multiple main characters - and don't even realize this is a story about Alexander the Great until the home stretch.
Problem is that fans have spent several years hyper-analyzing every aspect of the books/show so they expect more grand surprises. It almost undermines how pivotal it was to find out that Jon is indeed the true King. We have 5 episodes left. If this thing doesn't land on the conclusion of his arc, it would be really bizarre storytelling that would feel random and "twisty" for the sake of being twisty.
I binge watched GOT two years ago, and must say my thoughts are not nearly as informed. I know nothing about the books.
Conventionally, I think you are correct; that Jon is the ultimate protagonist of the story. Yet I am not so certain that Jon will both win out and survive in the end. Certainly that would be the most satisfying end in the conventional sense of story telling. The writers, however, do seem to relish doing the unexpected. And it is not at odds for the protagonist to die in the end and still get what he wants, sort of. Good example is Walter White in Breaking Bad, which had a very satisfying ending in the view of many including mine.
I am also somewhat cynical about the influence the "Me Too" movement (which occurred during the filming of the last season, I think) may have on how the writers decide to conclude the story. I would be very surprised if the ultimate ruler in GOT is not a woman. Jon is not the only character with an arc, although he clearly is the spine of the story, as you have pointed out. Several of the leading women, other than Cersei, have experienced significant growth or arc through the episodes, so it would not look completely out of left field were this to happen.
So somehow, I see Jon's quest being satisfied (defeat of the white walkers, night king, the Lannisters and restoration of order), but through sacrifice where he probably dies, and a powerful woman ends up in charge. I could see the Kingdom being split into two parts, with Sansa ruling one part, and Dani the other. Maybe also introduce the concept of a democratic republic where citizens can elect a representative body of government. This whole concept of family rule seems destined for extinction.
And I would be fine with that.