I would have expanded the first part by a hundred or so chapters and had team seven take missions that lead them to the other villages. Get more background on the shinobi world and all. Sasuke can still leave in the end, but I would have had the sound four (Obviously not Kimimaro) survive and continue to serve as Orochimaru's bodyguards.
For part two, I would not have had Sasori be killed right away. He would have faked his own death or some BS to survive that fight. Hidan and Kakuzu would also survive a bit longer, especially Hidan. He really needed more to him other then "Lol immortal". Those two in the end would be the first defeated Akatsuki duo though.
As for the whole Sasuke vs Orochimaru fight, I would have the sound four come back into play here (And possibly the Naruto kyuubi vs Orochimaru fight too). Sasuke would be pushed to his limits fighting all four of them at the same time, but would eventually kill them all and then have that joke of a fight with Orochimaru where he does absorb Orochimaru and gain some temporary buff.
Upon hearing this, Sasori and Deidara would then be sent after either Naruto and company, or Sasuke + Hebi. I'd have Deidara still go after Sasuke, but this time around he would rely more on his teammates and basically make Hebi useful. Sasori would confront Naruto and company shortly after Kabuto comes on the scene and gives them the notes. Giving them a cheap advantage against him, but they would fight and Sasori would lose, though he would show exactly what he is capable of this time.
Now, the following Akatsuki members would gather: Pein, Konan, Zetsu, Kisame, and Itachi. Obito would NOT be a member. He'd be more of a fraccion/lacky for Zetsu, but I'll get back to that later. I'd have Pein personally order Kisame and Itachi to deal with team Hebi and then order them to get capture Naruto. The next events would basically be canon for Itachi vs Sasuke. Including Orochimaru's breakout, though he'd push a HEALTHY (yes, Itachi would not be crippled by illness) to his susanno limits before being sealed. Jiraiya vs Pein would also be the same as canon.
At this point, Zetzu and Obito arrive on the scene and kidnap Sasuke and Hebi. There Obito and Zetzu are more of spying on Akatsuki, while hatching their own nefarious plot. He would, again explain what Itachi went through and Sasuke would join the two. Again, more on that later.
With the death of Itachi and team hebi escaping, Pein himself attacks Konoha just like it was in Canon. The fight would be pretty similar, though he would hint at his pains earlier on. And in the end he would not be able to let go of them, and Naruto would kill Nagato. Kakashi would survive, though Shizune and others would remain dead. Konan would offically leave the akatsuki and that would end part 2.
Part 3 would start with Obito, still going as Tobi, openly calling himself the will of Madara. It would be revealed to us that several Uchiha over the ages agreed with Madara and left. There would be four to five Uchiha with three tome sharingan aiding Obito. Minor villages other than Amegakure would be tricked/leaders replaced and would fall under the control of these Uchiha. Tobi and Zetsu would confront Kisame and after a brief fight, Kisame would be recruited to join this new group. Tsunade would be in a coma longer too, but the Kage arc and the Sasuke vs Danzo fight would be the same. Without the attack on Karin though.
Naruto would NOT get control over the Kyuubi. I think that controlling the bijuu inside them should be strictly Killer Bee's thing. Naruto would advance Sage mode more, and be more powerful that way. Kabuto would join the side of the Uchiha/minor villages. Kisame would confront Killer Bee as in canon, though he would come closer to capturing him and when the Raikage arrives Kisame would be forced to flee somehow. Once the war starts Kisame would fight Gai to the death, both of them dying when Gai is forced to use open the 8th gate.
Kabuto would help in the war, summon the edo's and all that. The war would be similar to the one we see but it would be the major villages against the minor villages+edo's. The Uchiha generals would all be taken down by a Kage. Madara would be summoned, he would NOT have the rinnegan. The rinnegan would remain exclusive to Nagato and Obito once he steals it. Itachi would break out, Sasuke would find him and they would defeat Kabuto together. Without Izanimi. The Juubi would be summoned through some other carrier. NOT Gedo Mazo. Obito would be revealed against Kakashi, Bee, and Naruto (Possibly Sakura).
Madara would defeat the five kage with a high difficulty before going to help Obito. The Juubi would be summoned/released against the ever growing number of enemies for the Uchiha. Sasuke and the Orochimaru/edokage stuff would stay. Obito, like Nagato, would realize what he did was wrong near his death and will give his life to try and fight Madara. The kage would then seal Madara up after a long fight, and the Juubi would be dealt with through some group death reaper seal or some shit.
