Happy you enjoyed the experience. Was a big fan myself.

dislikes:
-If i hadn't seen egoraptor's mega man episode of sequelitis i would've broken the game trying to get fi out of it. Luckily everytime she said something useless i heard "mega man mega man" in my head which was hilarious.
- I like the motion control, but i could've been better. I was able to get better swordplay out of Red Steel 2 and better archery out of wii-sports resort.
-biggest complaint- You should have been able to travel to different ground areas by foot. You uncovered it all, why not go on a huge adventure?
-much like twilight with it's damn bug hunts, i hated searching for stuff in the creepy zones with statues. the activity was boring and annoying, but the setting was sweet.
likes
-favorite, most epic ending battle of any zelda ever. The scenerey, the dialogue, the setting, the music. Sweet jesus i had shivers the first time i tried to destroy demise.
-storytelling- this was the most in depth we've ever seen zelda and link. I also got a feeling that zelda and link have some sort of romantic relationship in this one. Something that was always just out of reach in past entries. This was the second best use of secondary characters in the series thus far.
- controls- bowling bombs were sweet.
- you were one form of one person the whole game.
-loved ghirahim's character. wish his costume design was a little more menacing.

There was a game breaking bug in the part of the game where you have to collect the three songs from the three dragons, I don't quite remember exactly how it was, but I believe if you went to the desert dragon first, then the bug would occur. Nintendo released a patch for this, and I think in the later copies of the game the bugs was removed.

You are near the end of the game.

It was if you went to the Thunder Dragon first, and then talked to the Goron that was standing just outside of that room.  Then the special events would not happen when you travelled to the other locations.

I forgot that you don't start a thread about Zelda and then get too busy to check it within the next 24 hours because the responses would have piled up. Your post seems to reflect the general responses in this thread. As for the things you don't like, as the OP, lemme give my OPinions

• I guess I've learned to ignore slight annoyances in games I like. Fi is more annoying than Navi, has a robotic personality but she can also be more useful than Midna occasionally. She states the obvious too many times, but she makes up for it when I want to know my game time, how many times I've slaughtered a particular enemy or some other useful info, since you actually have multiple options on what to ask her. Also, I did find her obsession with Bokoblin underpant funny. No matter which kind of Bokoblin you scanned, she'd chip in something about its undergarments.
• Yeah, the sky wasn't packed with activity, but it did a decent job as a hub world. Could have been better, but it wasn't terrible.
• Seeing as you're limited to the sky at night time, it has the same problems as the rest of the sky sections. Could be better, but it wasn't terrible. You could easilly ignore it.
• The flooded forest! Many of you didn't like it but I loved it! I'm an artist and seeing such a beautiful forest under water (clean, clear water) just tripped me. Maybe I would have been bored collecting tadtones if I didn't think the place looked so gorgeous. I knew it would revert to normal after I caught them all and I was wishing there was a way to replay that challenge just like you can the boss battles and silent realms, just so I could admire the artistic beauty of that segment again.
• Re-reading the description of collectibles all the time. Probably the most annoying aspect of the game to me. We should at least have had the option to speed up the text.

Yeah, as much as people complain about it, I liked the tadtones part. Was a cool way  to put a twist on a familiar area.

@MythMaker, you CAN skip any cutscenes you've seen before. And I don't get what you mean by motion controls aren't needed outside the boss fights. Unless you want to stick to bombs and arrows only, you can't kill almost half of the enemies in the game without swinging in the right direction. Just a few days ago, I laughed my ass off watching a Bokoblin block all of my brother's attacks for about 20 seconds straight!
You know what surprises me about people complaining about "forced motion controls" in some areas? I realize that these people over the years must have so perfected the use of the analog stick that the easier motion controls are actually harder for them. During the time it took me to beat Skyward Sword, I've beaten like 4 games on my PS3 (If I know I'm only home from school for a week for example, I'll play PS3 games because they're shorter). Many times I wished I could use SS controls on those PS3 games. Prototype 2 didn't make me want motion controls but controlling the remote controlled Batarang in Arkham City was painfully difficult. Just a few days ago, my brother who is on a God of War marathon (he just beat 1 and 2 and now is almost done with 3) was swimming and since he had played SS just the previous day, he was wishing for the motion controls while swimming in GoW.
You know what I've learned from all this? As an aspiring game developer, I'll make my control options as flexible as possible just in case. Like if I made SS, motion would be required for lots of things, but then for everything besides the sword, you would have the option of switching to classic controls. Even for aiming (who knows, someone out there might prefer classic aiming to pointer aiming). At least they did that to some extent in the game. You could select menu options through both control methods.

I've never had a problem with any of Zelda's helper characters, and I don't really understand it.  I didn't even know Navi was considered annoying until hearing complaints on an internet forum years later.

Yeah, though the problem with Fi isn't necessarily Fi; it's lazy programming.  I caught a bug before, you don't have to tell me every single time I catch one (Or restart the game, I can't recall it was almost two years ago).

I also didn't find Navi annoying at all on my first 2 play throughs of OoT. She's only a bit annoying on 3DS when she suggests that I take a break from playing. And yeah, I really don't understand how a problem like telling us what each bug or collectible is, each time we restart the game, WITH SLOW, UNSKIPPABLE text and animations managed to get past all the play testing they would have done before the game was released. But I have to admit. Fi does state the obvious far much more times than any previous helper character in the series. The worst part is when she/or someone else just told you something in a cutscene, only for her to come out and repeat that same piece of information immediately after the cut scene!