If this game was to be made then the stories I feel that need to be explained would Mickey's story from the start of KH1 to right before he is able to finally physically join Riku in Castle Oblivion during CoM. The final boss for this story would be the Red Eyed Heartless that Aqua fought in BBSFM. After the battle, a bright light would blind Mickey and take him to Castle Oblivion. We all know what happens inside Castle Oblivion so after the battle with Red Eyes; that story should end with Mickey being blinded by the light and then calling out Riku's name to save him from the darkness. It never shows them actually meeting though.
The second story I feel needs to be covered is Riku's story after CoM. Mickey will accompany him for a short time, but like Mickey said in KH2, they got separated. Some of this story will be in unison with Days such as fighting Xion and Roxas and the story may end with Riku defeating Roxas or the story may go on a little longer up until when Riku gives Sora the picture of Roxas and the Twilight Town gang and the sea salt ice cream. That would be the latest that that story needs to go.
The reason Riku's KH1 story and Mickey's KH2 story doesn't need to be told is because they were much more prominent characters and we knew what they were doing for the most part in those games.
Lastly, Aqua. BBSFM pretty much covered what she has been doing. She has been traveling through the Realm of Darkness looking for a way out and fighting Heartless along the way. And according to the meeting she had with Ansem the Wise, it has been 10+ years. Her story would not be exciting at all and would give no new information. If they do make this game and want to add an Aqua scenario, then the player should have to beat Riku and Mickey's stories first which would then unlock the short extra Aqua scenario that was playable in BBSFM so the Americans who more than likely have never played FM could then play it (like me).
Final Bosses would be: Red Eyes (Mickey and Aqua) and Roxas or Red Eyes (Riku).
Worlds: Mickey- Traverse Town, Hollow Bastion, Disney Castle, Realm of Darkness, and Olympus Coliseum (Underworld). Not sure what others.
Riku: Twilight Town, Data Twilight Town, The World That Never Was, Castle Oblivion, Hollow Bastion/Radiant Garden, Olympus Coliseum, Land of Dragons, Disney Castle, and the Realm of Darkness. Not sure where else.
Aqua: Realm of Darkness and the Dark Margin. Nowhere else.
Interesting Things- Playing as Mickey Mouse. Playing as Ansem-Riku. Using the Guardian. Corridors of Darkness and the Realm of Darkness. Obtaining the Kingdom Key D and transforming the Soul Eater into the Way to the Dawn. Seeing the characters who played the background of KH1 and KH2.