DemonFiccer: I don't think anyone liked it when I decided to wipe Kumo off the face of the Elemental Nations, but then, the destruction of Kumogakure would not have had as big an impact on people if they didn't care. That's really the whole reason I wiped the hidden village out. I wanted to create some tension and drama, as well as give the Main Characters something to grieve about and some emotional hardships they will need to overcome. I guess you could say it was done for the sake of character development.
As for me changing A's name to E, I honestly have no excuse for that. I think it was just a slip of my fingers.
Firetemplar415: It's not so much that I am adding yuri as I am showing you how the girl's (Yugito and Mei) act in Naruto's absence. I believe it's important to see how they would act around each other when Naruto isn't there, otherwise Mei and Yugito, who are very important characters in this story. I don't want them to become background characters whose only purpose is to let Naruto stuff his phallus in their every orifice like a good deal of other fanfictions tend to do.
Why kill off Bee? Because the heroes have had it to easy so far. Anime logic dictates that when too many good things happen, something equally bad needs to happen in order to give the story a sense of suspense. It's no fun to read something that's all fluffy bunnies and rainbows.
Cerulean Knight: Naruto actually does not have Fu tagged with a Hiraishin seal, though she does have one of his Kunai. No one actually has the Hiraishin seal on them, even his wives only have it on their rings. The reason for this is because when the Hiraishin seal is activated via chakra, it creates an imprint within his mind that he is constantly aware of, sort of like a buzzing in your ears that only you can hear. And since humans always have a set level of chakra circulating inside of them the seal would always be active. Could you imagine how annoying it is to have that constant hum in the back of your mind all the time? I couldn't.
SSJ3 Kyuubi Gohan: Without giving away too much information I can say that Aizen will have a role to play beyond “kameo appearance” much like all the other Kameo's I have in this story. Whether he will be good or evil I cannot say.