Well, I m new, but I think that you are exagerating all of this:
1- Yen Sid cant use time travel, he simply used is magic to revert Sora and Riku´s abilities to 0. Of course, at 14-15 years old they had not started their journey, so he reverted theme to this original state. No time travel was used.
2- If you think a little, you know that Ursula is not alive, so obviously that Ursula is not the real Ursula. It was not explained, but it is very possible that Yen Sid created that phantom to test Sora and Riku.
3- If you recall, once they opened the Kehyhole wich was under the sea, they entered the sleepy Traverse Town. So is very plausible to say that it was the entrance of the Realm of Sleep, witch Yen Sid prepared.
4- Well, if Traverse Town was divided in two paralell dimensions, its logical to think that its keyhole has been divided in two as well. That would explain why all the sleeping worlds have the same division. Its just a Theory, though.
5- As I recall, the characters that apear in the Sleeping worlds, could not be real. ¿Why?, because it seems that the worlds are dreaming with the last events that happened before they fell in sleep. That explain why Mickey and the others appear in these worlds: because these events happened just before the world became a sleeping world. In fact, Country of the Mouskeeters explain when did Mickey met Minnie for the first time. It also seem that that world was the homeworld for Pete, Miniie, Donald and Goofie, and when they left the world, it became useless and started to fall in sleep.
Traverse Town can be an example as well; the world was special because it gathered all the peolpe who was lost after their worlds were destryed by the heartless. So, when Sora and co defeated Ansem and the worlds were restored, Traverse Town lost its function, so it became a sleeping world.
6- Thats a long one: First of all, TWTNW was destroyed after the defeat of the Organization; in KH2 if you remember, the castle was falling at the end. Also, why is now a sleeping world?. Because as the other worlds, TWTNW lost all his fuctions when the Nobodies were defated. And for the rest, you should remember that Sora was in a dream, Xigbar and Xemnas were manipulating him to go deeper in his sleep and even was put in a second dream. Why all these strange things and change of forms?. It simple, all is a DREAM, in dreams all what happens is illogical. Xigbar and Xemnas were manipulating his dreams, also all the conections within Soras heart started to be seen in his dreams because it was the perfect moment to be shown. As Sora was going deeper in the dream and its second layer, all was being far more subrealist than before. Riku didnt saw nothing of this because he never went deeper in his dreams. Its that and nothing more.
7- Well, Xion never went to Roxas, her existence went directly to Sora. Braig wanted to defeat Terra to get a Keyblade, remeber?. Roxas got his second keyblade for defeating Xion, not for having her heart.