Skyward Sword is my 4th Favorite Zelda, and I do love the game (felt it had a strong plot, the colors made it very pleasing to the eyes, had some great bosses, a lot of sidequests, etc.), but I do see why people don't like it.
While a lot of people don't have trouble with the Wii Motion Controls, they still can be very janky to the player. There were a few times where it would glitch every so often and have to recalibrate it more than I wish I did, but I was fine with it for the most part. What I think Nintendo didn't realize was that everyone in the game shouldn't have had motion controls. I mean, they basically were like "all or nothing", and a few of the actions could have been just normal movement of the control stick or something. One thing I realized those from watching my sister and mother play the game is that they consently fought against the motion controls and had ton times in certain areas of the game. Plus - which I had a problem with the first time I played through it - there's a lot of enemies/bosses that require you to wait and make a specific strike at a specific spot in order to damage it. A lot of people (and me when fighting the final form of the last Ghirahim battle) just feel pressured to just act quick since in previous Zelda games enemies were a bit more fierce and didn't wait for you to attack as quickly as in this game. The motion controls was a great concept, and there were many points in the game where it was great, but veterans of the series that were used to just swinging the sword as soon as possible were a bit taken by surprise, so it was like relearning how to battle in Zelda. Newcomers may have had trouble but I think since they never played Zelda before, they didn't know what it was like before.
Another issue a lot of people found with the game is that it was like going in circles most of the game. You go to Faron Woods, then go to Eldin Volcano, then Lanayru Desert, then back to Faron Woods, then Lanayru Desert, then Eldin Volcano, then back to each area again to get the Song of the Hero, then back to Faron Woods again (that's just the macro outline; there are many points where you visit each area over and over in those mix). The overworld really wasn't that huge, and made it rough having to be in the same three places for the entire game, having little change except maybe a new area or two. It was pretty tiring having to constantly go back to each spot, go down the same paths, and spend way more time than you would in other Zelda games. Not to mention that each area was separated from each other, and not connected whatsoever, so you had to fly in the air to get there, and speaking of flying, there was not much in the upper-world to explore and flying took forever to get from one destination to the other. It just got boring flying from Skyloft to somewhere like Beedle's Isle or Isle of Song and just seeing it in the distance but having to take like 3 minutes to reach it while you just sit there doing nothing but making sure your loftwing is stable. Traveling definitely was a bit of an issue in this game, as well as barely any changes between the areas when you revisit them, making it just repetitive.
And of course people complain about the handholding, especially from Fi (even though I loved Fi; at least she was unique). I mean, besides the stuff from Fi, there was a lot of handholding, and not so much exploration. It's like "okay, here's drowsing ability; don't explore, just go straight to where it is pointing". And then every time you start up the game and you grab one of the million like Amber Relics lying around and having to re-read what they do. I know TP did this with the Rupees, but at least there is not a billion little trinkets you can get and just having to go through every one each time. I will say that there wasn't a point where I didn't feel lost in the game, but that's not neccessarily a good thing, because one of the many things about the other Zeldas is that sometimes just traveling and exploring will answer your confusion, and you really get to feel the area, and Skyward Sword definitely felt like "Go from Point A, now Point B, now Point C, back to Point A..."
I think overall while it had many strong and great things about it, there was a lot of things that one could nitpick about the game. I definitely wanted to say I loved the game a lot more, but there are a few glaring things about the game that just bring it down. There's a ton to do in the game, but it feels like this game you travel more than you actually do stuff - more than a lot of the Zelda games. It's not that big of a world compared to other games, and revisiting every place like 4-5 times (mandatory), it's get very stale. I think the biggest thing Skyward Sword faced was that a lot of points in the game made it feel like a chore rather than having fun, and it was just going through the cycles of "okay, let me go straight from here to there since there isn't really anything else I can do" rather than actually having fun in those sections.
EDIT - I agree with Nabber that this was an experimental game. It took a lot of risks, and some paid off, while others kind of flopped. There definitely was a lot of really strong points in the game, but there was also more noticable flaws about the game due to it.