The unconnected regions in Skyward Sword was one of the biggest dissapointments for me in that game and it shouldn't be implemented again.
First of all, it agrivated me logically. Now, I know you can't think logically in a video game, especially a Nintendo game, but this seriously made me angry. How is it even remotely possible for there to be three separated land masses on the ground? I'll stop this argument shortly because I know it's invalid but it just bothered me so I thought I'd throw it in there.
Now, thinking in terms of game design, it was a poor move by Nintendo. Constantly going to a bird statue to fly up into the sky then having to go to a different location really got old fast. Why couldn't there just be a simple three-way access point through the land areas so we wouldn't have to constantly fly upwards and downwards? It would make the game feel more realistic, fluid, and overall more enjoyable. I really envy Ocarina of Time's overworld so much because Nintendo managed to capture this idea perfectly. Hyrule field was the main focus point but all areas seemed connected and easily accessible which made for a real smooth adventure the whole way through.
Now, the main concern people had with this idea was that Skyloft would have been neglected because if people could access all three areas on the surface then there would be no need to fly back to the sky and visit Skyloft. I don't agree with this at all. You had to visit Skyloft two times to return the stone plates you received from visiting the surface the first go around. You then had to obtain the three songs by going into the Isle of the Goddess. Then finally, you had to go through Sky Keep. Those are all instances where you had to return to the sky in the main quest alone. Don't forget about all the lovely sidequests that were available to you on Skyloft that would motivate you to go back there on your own.
In terms of revisiting the same areas over and over again, I also don't like that aspect of the formula, but I think it worked for Skyward Sword. If the game made you fly thousands of miles to make you go to 10 different surface areas then that would feel like the game was trying too hard to be big. Revisiting the same areas with different objectives worked for Skyward Sword and I was content with finding all the cool areas I gained access too after completing more of the main storyline.
One thing that I thought Skyward Sword did right was with the item development. A Zelda game doesn't need 43534756 different items for the player to obtain only to use each item two times throughout the whole story. In Skyward Sword, we had a select few items that were developed creatively that we used multiple times throughout our journey. That is what Zelda needs and I hope to see that in Zelda Wii U