Best? I'd have to say no. JuicieJ said it quite well for me. I LOVE Skyward Sword -- it's definitely one of my favorite in the series -- but "best" is a very broad claim. ESPECIALLY best game of all time. There are several flaws and many arguments people have against it are really solid. It has far too many problems. For example, the music, I have to agree, wasn't fantastic, although I have a TON of SS songs on my playlist. And dungeons were... meh. Returning to areas wasn't particularly fun. I especially thought the Earth Temple and Fire Sanctuary were incredibly boring and repetitive. (But hey, the Earth Temple had one of the best songs in the game, so there! XD) And the sky... was one of the biggest disappointments ever. Its map look so much like TWW's overworld, and I was so excited to explore it... but then it was so empty!
But that's not to say that it's not worthy of praise. SS's greatest strength is its storytelling. Note that it's not necessarily its STORY, which had so many plot holes and inconsistencies it was rather ridiculous, but, my gosh, its ability to create emotion was somewhere the series hasn't really been since Majora's Mask. Its cutscenes were cinematic, exciting, and realistic. The villain may have been a flat character, but his appearances were so well implemented into the game's story that it felt like such a huge improvement from previous adversaries. Link, Zelda, and many of the supporting characters felt more alive and relatable than before. Groose's characterization was impressive for a Zelda game.
Most people seem to use linearity like an insult these days. And, first of all, it's absolutely ridiculous to say SS is more linear than Twilight Princess -- since, you know, it actually had choices toward the end of the game on where you wanted to go to get the Song of the Hero parts, and different lines of dialogue depending on your responses to certain questions. ...But yeah. I saw nothing wrong with the linearity it presented. It gave me a good story.
The problem lies in the fact that many Zelda fans don't like that. And if you don't care for cutscenes, story, characterization, or anything like that... you're probably not going to like SS.
Or if you hate motion controls. You might as well not even try the game in that case. XD
Speaking of which, I never had any problems with the motion controls and I LOVED them. That's why I enjoyed the game so much; I felt it was the most immersive Zelda game ever thanks to its storytelling and control scheme. Like I think the OP said, combat in that game actually felt like a skill you had to master. I think they probably could have progressed the difficulty of the enemies a bit better, but... eh. I still enjoyed it. Shielding took me forever to finally get the hang of, as well as using backflipping and sidestepping effectively. Demise's fight was SO amazingly fun. I had to find the perfect strategy and time my shielding JUST right, and then make sure I sidestepped his beam attacks and backflipped the charge attacks... Man, it was great. XD
So I think I've gotten completely off-topic right now and quite honestly I have no idea where I was going with this post so, uh... SS is awesome. But certainly not the best game of all time. There are too many things that could have been done to make it better.