Actually, Hyrule Historia hints that the Ocarina of Time is in fact made from Timeshift stones.
http://forums.zeldainformer.com/threads/hyrule-historia-translations.8624/page-5
Read the first two posts.
Impa chastizing Link, Groose falling out of the sky, Ghirahim in the Fire Sanctuary, Link travelling through the Gate of Time for the first time, the epic Triforce wish, Ghirahim kidnapping Zelda, and every Ghirahim scene in the finale.
My favorite thing was rolling bombs at the bokoblins/moblins, watching them back away, and then whipping out the gust bellows and blowing them at them. Felt so good to outsmart their AI.
Wind Waker's dungeons were much simpler. Skyward Sword had more streamlined dungeons. They were shorter and there were no branching paths or extra rooms. This might be where you are getting the impression that they are simpler.
It is impossible to miss the clawshots. If you think you missed them, then it is not time to get them yet. This is a very linear game. Just follow the path the game lays out for you.
Well if I recall correctly, Skyview had alot of bird architecture throughout the dungeon. It was also probably created to protect the sacred spring, which would be the first place the goddess reincarnated would travel to after falling from the heavens. So the place has its connections to the...
Honestly, I'd download Ocarina of Time and Majora's Mask off of virtual console. It would only cost $20 total. These two games represent the pinnacle of the series and pretty much define what a Zelda should be.
But my next choice would be Skyward Sword. Great game.
Some people are labelling this game as the worst because it brings the most change. Some people will reflexively shy away from it. With a game like this, only time will tell how good it truly is.
The sword Ganondorf uses in Twilight Princess is the sword that the sages used for executions. We see him obtain it in the flashback at the end of Arbiter's Grounds.