I have some scattered thoughts that I just wanted to post. This will be incomplete without more information that will come out of Kingdom Hearts Union Cross and future titles, but I feel as though Xehanort is even more in control of this saga than even the Masters of Masters in some ways.
Spoiler ShowI feel that since the grand reveal that Braig/Xigbar is actually Luxu, a lot are speculating, not necessarily on this forum, that he was controlling or influencing Xehanort. I don't think this was the case at all. As far as we know, Luxu was simply meant to ally with the Dark Master and keep observing. There were probably even moments when Luxu questioned his own role (such as being stabbed with his own Keyblade). However, what appears to be more intriguing to me is how much Xehanort appears to know about the past. Xehanort always seems to know what everyone else is up to, but does not always reveal his hand, instead repositioning his plans around that betrayal; he doesn't presume to trust anyone except himself, including Braig.
From what it appears in BBS, Xehanort approached Braig, rather than vice versa, as he did with Maleficent. The odds of him locating Luxu's last vessel are incredible, unless he knew something all along. Braig was a bumbling guard with a sarcastic wit, so why would Xehanort choose him to be one of the carriers of his grand contingency plans? At first, it seemed because he was in the perfect position to exploit Ansem the Wise's research and apprentices, but perhaps that was just the icing on the cake and it was more than that. I think Xehanort knew about Braig's true origins, just as he knew about Marluxia, Larxene, Demyx, and Luxord.
I feel this would explain why Xehanort thought Braig to be the perfect right-hand man; someone with a role dictated to him and in a position of authority around Ansem. How he knew about the other Org members being keyblade wielders is another story that I will get into a little later, but it couldn't have been through Braig. If Braig was the one who told Xehanort this information about the others, it would make his role far too obvious. He specifically acted oblivious to the Keyblade for that very reason, so he couldn't reveal crucial information about other keyblade bearers.
One possible scenario for how he found out this information on the other keyblade wielders (not Braig because he already recruited him) is through his experiments on Subject X (which I believe was Skuld) when he was an apprentice to Ansem the Wise. Though he did not gain access to her full memory, he learned enough to realize that she was from the past and traveled in time. He could have gained additional insights from this. This would explain why Braig rescued her from the prison; to prevent Xehanort from learning even more and damaging the MoM's program.
This could go even a step further with Master Xehanort doing the same thing to Ventus when he located him; probing his memory to learn more information on where he came from only to learn more about the ancient past. Xehanort lusted to become all knowing, so he wouldn't be able to resist learning about where Ventus came from. If he was successful and saw Maleficent in his memories, all the more reason he choose her as a pawn and reveal how to time travel, among much more (more on this later). In KHIII, Xehanort ordered his heartless to abduct Ansem the Wise and use him to locate the missing girl for her memory (they were already looking for Ventus for some time and Xehanort always likes to have alternatives to every scheme), which could reveal the location of the Black Box, among other information.
Then there is Maleficent. Xehanort revealed to her, in what appeared to be one heck of a lengthy conversation, the means to travel through time. We have yet to hear or see his reasons for doing this. Xehanort had a reason behind everything; from the recruitment of the organization members right down to their names, so this would be no different. Years later, once Maleficent served her initial purpose, Xehanort as a heartless, destroyed her body and gave her the means to time travel, which she immediately used to go back in the past and try to undo her defeat. I'm sure one reason is because Xehanort had more use for her in the future (using her to create more heartless for the Organization) and didn't want her permanently gone, but I think it's more than that.
Her time travel appears to be something the Master of Masters did not want, as he set up a digital version of Enchanted Dominion to trap her in. This is an important piece because it shows Xehanort making plans that that were not in line with the MoM's interests, illustrating that Xehanort is not his puppet. While in the past however, Maleficent learned how to travel back to the future, learning about the book of prophecies in the process. However, it is implied in the secret reports that the imposter Union Leader, who appears to be Brain, learned how to travel to the future by Maleficent, which appeared to be successful.
It seems that many of the Dandelions traveled forward in time by a plan of Brain's making, using what he learned from Maleficent (though they all ended up in separate points in time with no memories) and this became quite a benefit for Xehanort; four more members for his organization and another who became his first apprentice. There is obviously more to this that will be revealed, but I think Xehanort was playing a very long-term game here.
There's also the interesting fact that Xehanort knew about the gazing eye seeing the future, as he specifically looks at the keyblade in the opening when saying that. It makes me think that perhaps he was strategically using his keyblade when he received it to only show the MoM what he wanted to see and shape the future a certain way. This reminded me of an old interview with Nomura when he implied that Xemnas may be intentionally not using a keyblade. Perhaps this one of the reasons why. Most of his forms do not use a keyblade that often, so he may have been trying to show only what he wanted, especially since he was aware of the gazing eye.
Then there's the Black Box. I doubt Luxu simply lost it one day; he was meant to guard it with his life, so why is Xigbar looking for it if he knows its true location? It's because he really isn't, it's because Xehanort is looking for it and passed the order down to Xigbar to find it. The box was common knowledge in the organization, so Xigbar was not the only one who knew. Again, Xigbar could not have simply informed Xehanort of the Black Box because it would raise suspicions; Xehanort knew of its existence through some other means. Luxord said "they" only revealed hope is in the box, meaning it wasn't just Xigbar telling the organization about its contents.
Whether or not Xehanort knew Xigbar had the box is debatable, but it appeared to be hidden, and Xigbar ordered Luxord to find it and manipulated Maleficent as well to ensure Xehanort did not think of him as a traitor. Despite him being Luxu, I think Xigbar's fear of Xehanort was genuine, especially since his knowledge of the future was limited.
In order for Maleficent to believe something as grand as a "Book of Prophecies", she needed to see it/feel it herself. She did in the past; now that she knew the book existed, all that was needed was to plant the idea that is now existed in a black box. Xehanort was using her again through Xigbar to find the box, using an object he knew she coveted from her time in the past; time spent because of the information he gave her and his stabbing her with the Keyblade in KH1.
Finally there is the MoM; he has his own plans and agenda, which do not seem to be evil or good at this point. However, it does seem his plans have ended much differently than anticipated because too much was changed from the original program: Maleficent going into the past, one of the Union Leaders being an imposter, and the Dandelions going into the future. The last page talking about light expiring, that did not refer to the Keyblade War in X (that event was on the lost page as revealed in the secret reports), but the Keyblade War of KHIII. It did go as envisioned, until Sora came back and rescued all his friends, changing the course of history.
Despite this, Luxu completed his role, retrieved the Black Box from its location, and summoned the other Foretellers. His mission was to observe, independent of the result. The MoM will return, but will now go a different route, leading into the next saga.
TLDR; Xehanort was manipulating everyone to the point that it even contaminated the MoM's original program. How he found out so much will probably be revealed later, though I think it's most likely related to his experiment on Subject X, but I think this is a perfect scenario. Xehanort is still very much that grand strategist whose actions were rivaling that of another from the ancient past. With the Foretellers back and the MoM returning, plans have changed.