Aonuma confirmed that they were working on the overall balance during an E3 interview.
http://www.nintendoworldreport.com/news/27024
The Legend of Zelda: Skyward Sword is complete, and the development team is working with Miyamoto to fine-tune the balance, said Eiji Aonuma in an interview during E3 2011 with Famitsu. This process is taking some time due to the volume of it, and they have not yet had time to fully play out every part. Non-English translations are in progress as they hope for a simultaneous worldwide launch later this year.
The interview also discusses many of the story details in the game. The beginning of the plot has a different approach to the previous games. Zelda is a childhood friend of Link's in Skyloft, the floating city where he and his classmates attend the same boarding school. The town and its people are a focus of game events that often link to the main story. Aonuma compares this to Majora's Mask. Flying on birds is a staple of Skyloft, and the characters there know nothing of the mainland below. Link's rare red bird is special, since the other birds are unable to travel to the mainland.
New items will appear earlier in the game to make it more interesting. You need a certain basic set of items to navigate in the world, and that's why the unusual items usually come later. This time though, it was changed so you will be able to make use of items such as the the boomerang-beetle early in the game.
Ghiraham, the boss seen in the E3 2011 demo, is an important character who you will meet many times. He is similar to Dark Link in that he can see right through Link's moves and swinging your sword widly won't help you.
Lastly, the birth of the Master Sword is part of Skyward Sword, and the story links with Ocarina of Time and Ganondorf's appearance.
The news of the game's volume and the links with Ocarina of Time are promising, as previously Miyamoto has said that the future games need to be fun and less challenging to appeal to casual gamers, and in particular, Zelda needs to be more accessible. Historically, Nintendo have been reluctant to reveal Link's timeline and how the games relate to each other.