I like your theory, but i do agree that it might not leave room for KHIII Story. But my theory is kind of similar to yours...
I think that after the mark of mastery exam is over, Sora and Riku will start the journey to save the people who are hurting. They will travel somehow to the RoD and find Aqua, then from there she will take them to go see Ventus but once they get there they see that Ven's body is gone. After Aqua panics, Vanitas comes out and teases Aqua, Riku, and Sora with the basic "Looking for Someone", "Lose Something?" etc. Then it is revealed that Xehanort is almost fully revived and Ven is taken because he might still serve some use to Xehanort, then before Vanitas leaves he will give Sora and Riku a hint about they should go back to there island, and they go back and see Kairi is gone.
Then it would end in some other world and you see a body covered in darkness and it starts to become more visible and you see Xehanort rise and smile. Then the tiltle Kingdom Hearts III will pop up.
And just a quick thought, i remember Xehanort informing terra that he has many roads he can take to come back or something along those lines, as since we dont know what roads they are, i think a Vanitas return MIGHT happen. He's a very popular character, and i dont think Nomura will ignore his popularity.