Zelda is probably my favourite (or at least in my top 3) series, and I love every single game. I thought Skyward Sword was a fantastic game and that the amount it experimented with the "Zelda formula" was and is underrated by most people. It told a really compelling story, looked amazing for a Wii game, and was as inventive as any game in the series. It has some large structural problems in the second half of the game, and there isn't really a way around the fact that the motion controls had problems when it was released, and that those problems have only been exacerbated as time has gone on (I've revisited the game a couple times since and found them to be much more annoying).
Now that I've had a year and a half to think about it, Breath of the Wild is probably my favourite game of all time (or at least one of them). I loved the world, I loved the systems, and I even thought that the the story and the way in which they told it was moving and ingenious. I thought the Divine Beasts were a great substitute for the dungeons of the previous games, as were the ways in which the runes interacted with the overworld and the shrines. I understand why people are critical of those elements, but I have to admit being a bit confused by the people who fully subscribed to some of the knottier elements of the game (manually identifying landmarks, breakable weapons, many other things) but don't see the Divine Beasts and the memories as being of a piece with the rest of it. Oh well! It exists in my mind as a singular media/art object like the great books I've read, plays I've seen or movies I've watched.