They introduced the idea of the worlds appearing in the dark realm partially intact when Aqua discovered the undamaged Castle of Drams from Cinderella. In fact, she is walking the same clearing area where she fought the Cursed pumpkin carriage. They can have it where Aqua explores the parts of the worlds swallowed by darkness. They can also introduce new worlds for her to travel in the dark realm that were taken and then these worlds could be revived and more explorable in KHIII.
Also, there is Mickey in the dark realm that was shown, as well as Kairi in front of the old mansion.
I can see them doing a BBS variation with different playable characters, but spread it out over years. So, for instance, you could play as Aqua at various time points, maybe then take control of mickey or another character for a section. It could be like FFIV TAY.
With BBSV2 I'm expecting them to use something similar to a chapter based system. For example:
Chapter 1: The Heartless Experiments and Fall of Radiant Gardens
Chapter 2: Aqua's Time in the Dark Realm
Chapter 3: Mickey's Adventures during the 9 year gap
Chapter 4: The Organization's story during the 9 year gap (Though this one could be incoportated into other chapters)
Chapter 5: Riku's time with the Disney Villains and meeting Mickey in the Realm of Darkness
Chapter 6: Riku's adventures during the time of 358/2 Days
Chapter 7: Mickey's adventures during the time of 358/2 Days
Chapter 8: Some stuff with Aqua
Chapter 9: Riku and Mickey's absence during KH2
Chapter 10: Some mysterious story
Something like the above, perhaps they could even do a chapter on Eraqus and Xehanort when they were young apprentices.
The second idea would be where you select a character and their story is divided into chapters like:
Riku's Story:
Chapter 1: Time with the Disney villains and meeting Mickey in the Dark Realm in KH1
Chapter 2: Adventures during 358/2 Days
Chapter 3: Period of Absence during KH2
Aqua's Story:
Chapter 1: Time in the Dark Realm during the 9 year gap
Chapter 2: Perhaps something she was doing during KH1 and 358/2 Days
Chapter 3: Something she was doing during KH2 and then meeting Ansem
Chapter 4: Her finally being rescued by Sora after KH3D
so on and so forth with each character that is playable. Personally I like the second style of chapters better than the first. The first is usually better if you play as just one character in the story, and I think the first style should have been the course for 358/2 Days and the second style works better for BBSV2.