I know I'm not really qualified to speak compared to the rest of y'all given my slim knowledge and relatively low level fan status, but this is the internet, so why let that stop me because I'm pretty well informed and taught about art!
I think a lot of y'all including OP may be sort of...forcing a structure and expectations on this game that at no point and level does it seem like it is attempting to meet. I say judge a work on the target it chooses and how well it hits that target. No story has to follow a three or five act play structure to be good. And it can be purposefully disjointed because life is that way. Characters do not have to be relevant to the overall plot or indeed at all for a story to work as it is intended. Characters don't even have to have depth for them to be done well in stories.
To my second point first, how many people have you met in your daily comings and goings and even what you would consider your personal life character arcs that were totally irrelevant to the over-all story of your life? I would say this describes most people we all ever encounter. A story isn't bad because it reflects this fact or utilizes it. Link has no character arc and yet you all seem just fine with him. Savage Illia basically because you didn't spend an entire game running around in her skin? That's not fair. They're both equally thin characters with no real point. You could swap in any other character to where Link is and have the same damn story. Because it isn't Link's Story. Or Illia's. Or any of these other people's stories. And that's not a failing, it is a perspective.
Midna is the only real character in here. The entire story and arc of Twilight Princess is (aptly) about taking Midna from being a selfish doddling **** who doesn't care about anyone or anything to someone who is well, capable of great sacrifice for those she doesn't know or care about. You play the game from her perspective more or less. A disjointed series of unimportant and kind of annoying people who are in the way of solving her curse plus her loyal dog (Link).
You don't have to like it, but I do think this is on purpose and for me personally, it is kind of refreshing not to have this perfectly interconnected web of little mini and major stories that are perfectly orchestrated.
To my first point second, Twilight Princess is...pretty different from a lot of Zeldas. I think that's what draws a lot of us to it. It's pretty dark in tone, it is pretty weird at every level, and the word moody can be applied basically everywhere. It is pretty one of a kind in this respect. It certainly has the beats of a Zelda and isn't without all the references, but it has a haunted darkness no other game does.
And I bring this up because I think all of this together explains what you're calling the "shoe-horned" Ganon. Not all evil is this larger than life looming figure of chaos who you've known was the bad guy since the beginning of the story. In fact, most of it isn't that way. Most of it lurks in the shadows barely revealing itself until it has no choice. It's just in the air you breath and just out of your vision when you blink. It has pawns and puppets and plays games. And you don't know about it because you aren't that important or informed.
I love that the final boss is both not the guy you expect because he hasn't been in the entire game and also is the guy you expect because he's always the final boss. I think that's a stroke of genius actually.
P.s. This post was written in a purposefully disjointed fashion. You didn't notice it, but your brain did.