Shadao was right in how he addressed all of these concerns you had. It does feel like Skyward Sword has quite a few plot holes though. These could probably be explained somehow but here is what found to be a bit unusual. Please be aware of Spoilers.
1.) The Goddess Hylia only sent the Hylians up into the sky but left all the other races to fight by her side against Demise. Not really a plot hole, but how can the kikwis and parella fight against an army of Demons?
2.) When Link travels on the surface, it always seems to be a bright sunny day despite the cloud barrier which seems to mysteriously vanish when Link is on the surface.
3.) The Gorons don't seem to come from Hyrule as they are archaeologists yet they were mentioned in the intro fighting alongside Hylia. Maybe there homeland was wiped out?
4.) Link defeats Demise in the past, in which case would result in none of the events of the game happening since Demise would be dead and not return in the form of the Imprisoned.
5.) Skyloft, and many of the other islands in the Sky were sent up into the air by Hylia but there is no information concerning the location of Skyloft on the surface.
6.) Ghirahim has the ability to teleport yet he is unable to reach Zelda before Link. Why is this?
7.) If Ghirahim has the power to summon hordes of enemies, black tornados, blast through walls and create magical barriers then why doesn't he use these against Link in the boss fights. I know that it would probably make the boss fights too hard otherwise but I still find it to be ridiculous that he doesn't use his powers to his advantage.
8.) How did Zelda travel between Faron Woods and Eldin Volcano without Impa in the beginning of the game?
9.) Why does Link not have any parents? I could never find any information concerning them. They can't of died in the war against Demise because that was over a thousand years ago.
10.) When Link fights Tentalus, not only does it thrust its tentacles through the hull of the ship which would logically cause it to sink, but during the fight, it is clear that all of, if not most of the Sand Sea has returned to water, yet after the fight, back at the docks the Sand Sea is full of sand again.
If someone could explain these plot holes I would be grateful because it has really been weighing down on me since I found these out in game.
1. Humans simply suck and needed the protection of the goddess. Kikwis were able to camoflage themselves and the Parella had the protection of the Water Dragon, also, living in water makes them a harder target.
2. The sun can travel through clouds, and perhaps the cloud barrier was so high up that you can't see it from the surface. Other than that, it's not a plot hole more than the developers just saying "Do you really want to look at a cloud barrier all day? We don't care..."
3. Or maybe we just didn't see it? And being an archaeologist doesn't mean you're from an entirely different continent.
4. Time Travel - Don't question it.
5. The Goddess Statue was shown to have been part of the Sealed Grounds. As for Skyloft and the other islands.... who the hell cares? You could toss Skyloft into most openings and it would fit.
6. Ummm, because he doesn't know where Zelda is? That and Impa is blocking his opportunities for 3/4ths of the game. Besides, we don't know the extent of his teleportation and teleportation to unknown areas is risky in the first place.
7. Because gameplay.
Story reasons:
1st - Toying with Link, as stated.
2nd - Punishing him, uses super-sexy black arms.
3rd - Goes all out.
8. The Legend of Badass Zelda: The Journey from Faron to Eldin
-Coming Holiday 2013
There are rivers connecting the provinces, and it's shown at the end of the Earth Temple that Zelda can teleport a short distance after praying at the springs.
9. Ask every other Zelda game out there. Who knows, and who cares?
10. The Ship started to fill up with water, it
was sinking, just not immediately. As for the Timeshift stone, who knows, maybe the radius increased or something.
These aren't really plot holes. You're just looking way to far into things in terms of gameplay mechanics.