All jokes aside I guess the most serious mystery to me in DDD is the Mark of Mastery compared to BBS. Master Eraqus had two trials for Terra and Aqua. The orbs and then fighting each other. Yen Sid's test for Mickey was more vague. Aiding Ventus and Aqua, although disobeying Yen Sid, was enough for him to pass. Then in DDD Sora and Riku must save the Sleeping Worlds to pass by unlocking the 7 keyholes. The point is that there doesn't seem to be a traditional pattern to follow in making a Mark of Mastery exam. So how did Xehanort foresee that the exam would take place in the Sleeping Realm and knew to send YX there as a trap? It's not like the danger was widespread in the KH universe like the Heartless, Nobodies and Unversed which had to be dealt with. It was a separate realm and Yen Sid could have easily given a BBS type exam instead.
So does this mean that Xehanort had a spy collect intel on Yen Sid's plans and acted accordingly? Or, and this is my favorite choice, did Xehanort sent YX into the future to collect a Future Xehanort to join his new Org. 13? Think about it, how does Xehanort keep one step ahead although he loses or his plans are foiled in each game? He has FX to predict what's going to happen and Xehanort is able to continue his plans just using different paths to avoid himself being defeated. FX could have warned them about Yen Sid sending Sora and Riku to the Sleeping Realm and had plenty of time to make that trap. That's how he planned all the events to fall in his favor. So not only is Xehanort threatening the universe, he may be changing the events in time to suit his purposes. Quite diabolical of a plan if it was true.