In my experience every Zelda game after OOT was polarizing and seemed to be the most controversial one ever, during the first year or two of its lifespan.
TWW was "celda shit for kiddies", along with the usual list of random things it clearly did wrong.
TP was, in turn, held up as the result of everyone bitching over TWW, resulting in a "generic sellout game with shitty realistic graphics", along with many other complaints.
SS is just the latest victim of the modern Zelda Cycle.
Typically you have to let the games settle for a few years to get more rational discussions of what's good and bad about them. Right now, lots of opinions are conflating genuine design problems with matters of taste and preference.
For example, the overworld (NOT the skyworld) in SS is fine. There's nothing wrong with it because it's not one big Hyrule field to run back and forth across. It's merely a different concept for a Zelda overworld, and is one of the most refreshing parts of the game.
It is not, however, what some people would like to see. But that doesn't mean it's bad. That doesn't mean it's wrong.
By comparison, the hand-holding and intrusive tutorial system in the game is an objective design problem. The underdeveloped sky world is an objective design problem; it makes going back to the sky feel pointless and like an interruption to the game's compelling flow.
The technology around which the game is based is an objective problem. The tech isn't flawless. From there, whether or not it's "horrible" does involve personal preference and tolerance to a degree. Too many burned opinions are claiming it's basically non-functional and unplayable, which is clearly not true measured by how many people have played the game multiple times and learned to manipulate it deftly.
The complaints over 'fetch quests' and stuff like the spirit realms are a mixed bag. A lot of people have zero tolerance for anything that can be rationalized as 'filler', tho some of the reactions to it are way over the top. Like the people who claimed they played the game for 30 hours, got to one note-collecting swim, and thew it down to walk away forever. Seems just a bit hair trigger.
But, as with all Zelda games, we won't really be able to get a read on the aggregate opinion until a few years have passed. (And there's a new Zelda game to bitch about, ha ha.)
In a lot of ways, despite its flaws, SS is the best 3D Zelda purely (and obviously) because of Nintendo's experience. By this point, they're just a lot better at designing games around a 3D world. Most of the flaws in SS, IMO, boil down to only two factors: 1. Inherent technological limitations of the platform, and 2. Nintendo's hesitation in turning players loose without hand holding.