I predict Master Xehanort will be his own undoing as Gram said. Whether through betrayal from one of his vessels or negligence, he has made mistakes throughout the entire series yet has always been able to have a backup plan and/or improvise. That luck and flexibility can only last for so long. When it's all said and done, I think it will be a big risk to rely on his own versions of himself throughout time as they are all manipulative and selfish like him, opening the door to be a victim of the very type of deceit and betrayal that he has committed on others. (I think the YMX and Braig scene in Re:coded implies this, perhaps) MX has an uncanny ability to be prepared for every possibility, but he also got pretty lucky along the way as well, especially with the failure of Eraqus, Terra, and Ansem the Wise to realize what was going on behind their backs before it was too late.
I don't take AS strong of a view regarding DDD making Xemnas/Ansem or even the Apprentice irrelevant just because MX said it was him pulling strings the whole time because we have to keep in mind; he wasn't controlling them but rather he IS THEM. The post-BBS/pre-KH1 part of the story remains grey, but I think that there is a certain beauty to some things being left unsaid and to the imagination; here's my theory I've been thinking of recently of it all until we're told otherwise: immediately after Aqua defeated Terranort and he appeared with amnesia in Radiant Garden, I think Master Xehanort truly had amnesia, but like when YMX returned to Destiny Islands after time traveling, the memories of his past actions remained etched in his heart until they were awoken once more by the experiments conducted on him by Ansem the Wise and the Apprentices; they obviously didn't know (except Braig) that they were dealing with one of the most evil Keyblade Masters of all time who had taken over someone else's body.
After he and the other Apprentices betrayed and banished Ansem, I think it was safe to say that MX was back completely and, through both his prior knowledge and new knowledge gained as an apprentice with the others, he knew the attractiveness and viability of turning 13 Nobodies into vessels to represent the 13 Darknesses in the correct way (13 vs. 7 method) to forge the X-Blade. To split himself (and the others) into Heartless and Nobodies, he'd be able to start forming those 13 Darknesses (via Xemnas) and also develop yet another backup plan (via Ansem in time travel) in case it didn't work out. And he knew that once he had his 13 Darknesses, it wouldn't matter if he used the 7 Princesses of Heart or the 7 Guardians of Light to clash with as long as he had his side accounted for.