I don't wanna seem like I'm playing devil's advocate, but I didn't mind the motion control puzzles using the Pro controller. I think the ball maze puzzle was a weird puzzle to include (I do find it interesting the developers say the left the bottom flat so players could cheat on purpose), but all of the other ones are fine for me.
It was a weird adjustment since the motion control technology is different than in all of the various Wii controllers, I had a ton of moments at first where I was just leaning my controller or jerking it around and it wasn't doing what I wanted and it was infuriating. Then I realized I was just using it wrong and that it's very legitimately a 1:1 movement, and once I got used to that the puzzles were genuinely fun. Having a traditional controller and slowly spinning it around and upside down to control an object in 3D space that corresponds exactly with my movement is really cool to me. The motion controlled platforms and "light the torches" puzzles were actually some of my favorites in the whole game.