When Vexen Would Reveal His Plans To Sora I Think The Cutscene Would Of Ended Up As Sora Being Shocked By A Plan That Happened To Him By A Castle He Happend To Stumble Upon. Sora Than Would Of Spared Vexen, Forgiving Him, A Favor For A Favor. Even Though He Was With The Evil Organization XIII, He Would Think That There Is Some Good In Him, Not Knowing That Vexen Doesn't Have A Heart.
After This Sora Would Probably Sum Up The Strength To Go Through The Floors Very Fast, Not Forgetting Anything Else Because He Was So Determined To Destroy The Rest Of The Organization. He Would Make His Way To The Top Floors And Destroy Larxene And Then Marluxia. He Wouldn't Forgive Namine Because He Would Realize That Part Of The Enemy From Organization XIII Could Tell The Truth And She Didnt Even. Sora Would Not Go To Sleep Or Restore His Memories. Instead He Would Go To The Basements And Defeat Zexion And Lexaeus, Meeting Riku On The Way. They together would join forces to defeat the two remaining members within the castle walls.
Riku would not have gone with Diz because there is no need to now that Sora is still awake. Because everyones memories are in a chain, Riku would have not remembered Kairi Either, And all of Sora's friends that Sora has forgotten, he would never remember them again.
Roxas would have never remembered these memories with Sora, and Namine wouldnt help them because Sora would neglect her. Roxas' fate now lies with the Organization.
Vexen would have fled the castle returning to The World That Never Was. Returning to the castle, He would have told Xemnas about how Sora finished off everyone that was to weak and he was the only one left.
However Axel would of returned telling Xemnas that Marluxia planned to overthrow The Organization and Vexen told Sora about his plans. Vexen and Axel would probably rise up in importance at The Organization because they both stayed loyal to Xemnas and not Marluxia.
Riku and Sora would still be together finding the Organization's members defeating them one by one.
Roxas wouldnt have left the Organization and Axel And Him Would Still Be Friends.
Xigbar, Saix, Luxord, Vexen, Axel, AND Roxas would be the final bosses fighting in the castle.
Everyone would be destroyed INCLUDING Roxas. And Namine would have met her demise later. Both of them would have never become whole because Kairi and Sora dont remember eachother.
Roxas, Namine, The Rest of the Organization would have died.
Kairi would never reunite with Sora and Riku.
Sora and Riku would travel the worlds more because they would have no reason to go home. They would later die also in a battle they did not win.
Basically Yea, everything in the sequence in time flows together, rewriting one part means rewriting the whole sequence. That was fun writing. Maybe i should make a fanfic.