I went through the topic and I haven't noticed anyone else disliking Skyward Sword. I must be a minority. I still feel like explaining as to why I really don't like it.
First off, the Silent Realms. I've got lots to say about that. What they do is annoy me, and stress me out, mainly cause it is so easy to screw up by mistake and lose all the work you did when you were 1 teardrop away.
I don't like forced stealth missions, even if this isn't a proper one, it still technically is trying to be one. You're on a timer, too, something that I've always loathed in video games, much less when you have to do it MULTIPLE gods-damned times. I mean, Twilight Princess didn't bother me when I had to do it, but that's cause you didn't get one-shot back to the beginning every time an enemy touched you.
It's like they tried to combine the Teardrop quest from TP, with the "don't get caught or you go back to beginning" crap from Phantom Hourglass. I seem to recall most people couldn't stand that in Phantom Hourglass (and trust, no matter how much you might've liked it, I saw scads of hate for it all over the internet), but that might've been cause it also smashed the game's pacing.
I don't mind it being frantic or having to not get hit.. MUCH. Honestly, the whole section would be a hell of a lot less stressful if I didn't have that obnoxious stamina gauge. It's funny, I rarely notice the thing until I have to run like mad for whatever reason. I really think the Silent Realms could have been better if they hadn't made it a 1-hit-you-lose scenario, and given the player a couple of hits. Not the full amount of health you normally have, but say 3 hit tops.
I dunno, it just really irks me that they had something that could've been really nice and then they go and make it unenjoyable by having this forced "don't get caught" crap. It's just not the sort of gameplay element I think Zelda needs. At least in Wind Waker you could hide.
...actually, now that I think about it, if Link doesn't keep his Health or his Items as he's only there in Spirit, giving him that stupid Stamina Gauge inside the Silent Realm makes absolutely no sense, except from a "challenge" standpoint. If they wanted to make it a challenge, they could've just left that for Hero Mode and done without it.
Next is the overworld map. I'm not going to go into detail here because you've probably heard it multiple times already. It's the fact that they are not even connected. It's really a pain if you want to change province that you have to find a bird statue, select Go to the sky, fly to the desired location and then drop wherever you want to go. It might be fine for an hand-held but its not for a console game. And the fact that the exploration is non-existent doesn't help either.
The controls annoyed me just a little bit but not to the point where I need to say something about it.
This turned out to be longer than I expected...