I've got three that have been bugging me for a while.

#1: To put it simply, Obito dies when he was meant to. (i.e. at the Valley of the End) That alone completely changes the Narutoverse. Basically, I want to see a totally AU Narutoverse as a result of Obito's death. There are a million changes that could conceivably stem from that alone. Maybe Uzushiogakure was never destroyed, and Naruto is Kushina's bastard child. Maybe Akatsuki never got started, or just have different goals and members. Maybe the Kyuubi stayed safely in the hands of the Uzumaki. Maybe the massacre happened anyways, though possibly on a lesser scale.

Its up to the author, if this ever gets taken up. that being said, AU and Obito's death are my two sole requirements. The story itself could focus on anyone the author wishes, be they OC or canon. Keep in mind that, due to this being AU, any canon characters will be at least a little OOC, by sheer virtue of different life experiences. In other words, Sasuke may still be a little bastard, but if the massacre never happened, or only occurred on a lesser scale, he should be significantly less broody and vengeful.

#2: He may be a broody, revenge-obsessed little bastard, but Sasuke is no traitor- if only because his brother is the traitor, and he wants nothing to do with that crap. So when Orochimaru seals him and tries to lure him away, Sasuke flat out refuses. Cue shock from just about everyone who knows him. It can go one of two ways from there- either Sasuke can be shocked at the other's shock, and eventually get out of his funk (the character development route), or he can go on as he is, revenge-obsessed, but determined to be everything his brother was not (which could make a good plot on its own).

#3: For revenge purposes (specifics being up to the author), a group of super-smart civilian (or drop-out ninja) criminals with a major grudge against Konoha kidnap Naruto's graduating class. Why Naruto's class? Because it has the heirs to nearly all of Konoha's Clans. Because they are civilians, the criminals have no interest in/ little knowledge of the Sharingan and Byakugan. The children are tortured and then killed until only nine remain. These nine (the future rookies, of course- though you could substitute Sakura for someone else if she bothers you that much) having been slowly scraping together a plan, and just manage to escape before they are killed.

Whether they are able to make their way back to Konoha or are intercepted by a search party is your choice. Or maybe Itachi is just POed about what they did to Sasuke and anonymously helps them escape and get to Konoha. Either way, they all come back to Konoha traumatised and are put through therapy. This results in personality changes. Changes in the way of Shikamaru finding his motivation, Ino and Sakura(/OC) being broken of their fangirlness/general stupidity, Naruto learning the meaning of subtlety, etc, Sasuke deciding that the best revenge is living well (and/or coming to his senses about following a mass murderer's advice), Hinata ending up significantly less wimpy, and so forth.

I presume you can see how canon would be changed as a result of this. As for the kidnappers, you can have vengeful clans destroy them, leave them as a then-discarded plot device, or turn them into a nice long plot/subplot for the rookie nine. If they are turned into a plot, it may be better to leave Akatsuki out of things altogether- you can only have so many villians, after all, and having two powerful groups of them is quite the stretch. Summarily, rookie nine and classmates are kidnapped, and changes abound.

 

The first challenge is a problem because we don't actually know what Madara did after the Valley of the end yet.

 

500:1 odds he actually died there.

Doesn't really matter though, since we do know that he's definitely dead as of the end of the timeskip, otherwise Edo Tensei wouldn't have been able to res him. Obito was just using his name to ride on his coattails. He couldn't have really affected anything, even if he was still running around. Otherwise, it would have been big news when someone finally offed him.

 

Shoot. Forgot about that. :facepalm

 

Eh, you could always go with the "What if Tobi actually was Madara?"

At minimum, you would avoid the absolutely retarded plot twist of Obito making an appearance with a complete personality-180.