It's great that you enjoyed the game as much as you have. Reminds me of myself and Majora's Mask. I can't say that I think Skyward Sword is the best Zelda game, though. I personally put it quite far down the list for a number of reasons, which I'll briefly mention here.
The main issue I had with Skyward Sword was that of repetition. The world was so much smaller than in previous games, and so much more linear in its design, that there was no excitement to going to new places. This is because there was no exploration element present in the game. Once you had visited a location that was it, you had seen everything it had to offer. There is an attempt to inject some new life into some areas later on, like when Faron Woods gets flooded, and I did genuinely enjoy that, but one moment in a 30+ hour game isn't enough to make the world interesting. Going back to previously visited areas with nothing new to find or do made the game quite boring for the most part.
The combat suffered from a similar problem. The motion controls worked fine and were well done, I'll agree, but they were utilised so badly that I would have prefered the game to have been designed without them. Almost every enemy in the game, whether it be a bokoblin, a lizalfos, a stalfos, or a deku baba, requires you to wait for an opening in its defence and then swing your sword in a specific direction. Too many enemies rely on this simplistic method, and it even taints some of the boss fights, such as Ghirahim and Bilocyte. You just find yourself doing the same physical action over and over and over until combat stops being interesting. The use of the motion plus is also the reason why Twilight Princess's hidden skills didn't make a return (except for the shield bash and ending blow). This was a major disappointment to me because the combat system in 3D Zelda had been steadily evolving since The Wind Waker and to see it suddenly take a huge regressive step back was not welcome to me.
I didn't have any issues with the game's story, per se, but I did have issues with its villains. Ghirahim was a bland character in the game because he has no development whatsoever; he is exactly the same at the end of the game as he is at the start. This makes him uninteresting as he is 1-dimensional and seems separate from events rather than being involved and affected by them. Demise was handled much worse, as the game tried to build him up as a threat by just telling you he was evil and powerful. We are given no reason to fear him other than Impa tells us we should. We also fight against a manifestation of him, The Imprisoned, three times before we even learn his name. This just undermines the threat he poses as we have already proven stronger than him before we truly know about him.
There were many other flaws with the game that hampered my enjoymnt of it but there's no need to go into any kind of serious detail. The main point is that the game made the motion controls too much of a focus but made too little varied use of them. In the end, most of the game is repetition, of bosses, of enemies, of puzzles, of locations. There are few moments that stand out, like the aforementioned flooded forest or the time travelling boat ride across a desert ocean, but these are far too few to cut through the general monotony that is Skyward Sword. It's a good game, I did like it, but compared with other Zelda games it leaves a lot to be desired.
