I don't even think what you have listed is even true, however BoTW clears ToTK for me because it seems more focused on what you goal should be. Like I remember in BoTW, is you needed to scale a mountain but you didn't have enough stamina, you would leave , explore more, level up and come back. In ToTK, you could just cheese and build some plane or just ascend if possible. So yea, you could say the skills are better in ToTK, I wouldn't debate that. But I don't think it makes it more fun for the user, at least for me.
In the same vain, I think the building is just very unfun and a chore. I get this will be polarizing, some will love some will hate, but the building is by far the worst aspect of ToTK. I hate this type of mechanic in all games (like I don't think someone could pay me to have to play Minecraft). I don't find fun in spending 15 mins to build a car, plane, w/e to have it last 20 seconds.
Both games are unfocused as fuck, it's kinda the whole point of them, letting you do what you want.
Except in totk you can't go to the final boss after a couple of hours, i think you have a more "classic" structure with steps to do before facing the finale, so i think totk is a bit more focused than botw.
Most of the things i listed are facts except story, skills and maybe dungeons (but i fail to think anyone who can prefer the dungeons in botw).
You have more enemy types and slightly better bosses, more ways to travers the map, what you find during exploration is a bit more useful and long term and give you a better sense of progression (just upgrading the battery to use the zonai devices is better than anytjing inside botw progression wise), you have both sky islanda and depth, the new skills make puzzle even more free to be solved in unexpected ways, the companions were a great reward for completing the dungeons instead of just having new rechargable skills like in botw, too bad the framerate goes into shit even more if you use them (switch hardware fault, not the game).
Like i think tokt is definitely the better game, the problem is that like someone else said, the improvements really don't solve almost any problem from the first game so they don't feel like big upgrades.
You have more enemy but they are still easy and retarded as fuck and combat in general still suck asses
Better dungeons but still decent at best compared to the best dungeons on the market
Better rewards for exploration but still crappy compared to games with better loot and better sense of progression
Better bosses but just compared to the absolute trash that were the bosses in the first game
More varied traversal but what you build is too much physics based so unless you are a fucking car builder in real life it's probably not gonna be super fun to use because you have a fucking wheel half centimeter too much on the left...
Fun fact, i absolutely hate building stuff in any game, and totk was basically the only game where i KINDA enjoyed the process, not much building cars and airplanes but just solving puzzles in unexpected ways and making a bridge with trees to reach a place, that type of stuff.