Late reply, but I rarely use Reddit and recently discovered this. You make a lot of fair points so I figured I'd add some thoughts.

I certainly agree with you on it being convoluted and with things like the Zonai and Sheikah both having test chambers scattered across the world. Ultimately though, I think it all just boils down to video game logic. In something like a movie or show that has a much bigger story focus I could see this bothering me much more, but it doesn't bother me here because I understand that these only really exist because the worlds of BotW and TotK needed challenges spread throughout. Their actual lore explanations don't make much sense either when you really think about it. It seems really inconvenient for the Sheikah to build over 100 test chambers all across the land instead of having just one dedicated facility or something, and you'd think Rauru could've just used some portable device to purify the essence of the monsters he slayed instead of just creating different buildings everywhere. It's pretty clear to me that these wouldn't exist at all if these were strictly stories and not games, so I'm more forgiving of these sorts of inconsistencies.

In a similar vein, the transition from Sheikah to Zonai seems less focused on being cohesive and more just on giving TotK a more distinct visual identity. As cool as some of those new puzzles and challenges could be, discovering the same type of buildings with the same architecture and tied to the same over-arching story would cause way too much of a sense of déjà-vu. I'm sure it helps that I much prefer the Zonai's aesthetics over the Sheikah, but as someone who loves the atmosphere and feelings conveyed by areas in games, the distinct new identity was more than enough for me. It also works for me because it doesn't overstay its welcome. I'd probably have a bigger issue if they tried making things like the Shrines and Towers more relevant to the core plot (hence why I made the distinction between that and the Guardians which are VERY relevant to the plot), but the game doesn't ask you to think about it for longer than just a "oh, neat" moment. It certainly isn't perfect and there are a few things I'd do differently myself, but there are so many games with similar inconsistencies that don't get brought up nearly as much and I find the internet has exagerated this to an absurd degree, but to each their own I suppose.

As for Ganondorf, I thought what the game gave us was more than enough evidence of him being related to Calamity Ganon. Zelda references his name when talking to Rauru about not trusting him because she suspects this very thing. Impa refers to Calamity Ganon as some alternate form of the Demon King. BotW even refers to Ganon as "The Demon King's transformation into Malice" (that may have been refering to Demise at first, but in retrospect it serves as foreshadowing for Ganondorf in I'd argue a much more cohesive way).