I have been thinking on this topic all day, and wanted to include my own hypothesis to be commented upon.
I believe one possibility is the Mysterious Figure/ Unknown is Master Xehanort's Nobody, and have some supporting evidence to back up that claim.
1. As far as I know from my own research, the Mysterious Figure/ Unknown himself is canon, but the fights he could have with all three characters are not necessarily so. I believe it is entirely possible that a player may confront the Mysterious Figure with their character of choice, for game play's sake, but that only Aqua's confrontation with him is canonical. This means she could have confronted him at the Land of Departure before going to Radiant Garden, as the Mysterious Tower @ Twilight Town is so close to Land of Departure on the World Map.
2. We do know that individuals who do not fight in an ambidextrous manner, typically speaking, in the Kingdom Heart's universe can do so if provided an opportunity. (I.E. Roxas acquired Xion's "Sham" Keyblade, thus he could wield Oathkeeper and Oblivion. My theory on this is that Oblivion is created by a Keychain reflecting Xion's demise, and Oathkeeper by a keychain reflecting Roxas' promise to stop Xemnas. Anyway, Sora's Form Changes are another example of Ambidextrous fighting; however, that is seemingly directly related to his bonding with Roxas in KH2.) Knowing Xemnas can fight with two Ethereal Blades means that either Terra or Xehanort could, or both. My belief, solely for the purpose of this theory, is that Xehanort could. I believe this is because Xehanort developed the ability to use Ethereal Blades through his experimentation with controlling the power of Darkness. I know Xehanort's element of choice in 358/2 is Nothingness, but in a way, all the Org13 use the powers of Darkness. They all use the Dark Corridors.
2a. We know Xehanort experimented heavily with his control over Darkness, as seen in Birth by Sleep and the Xehanort Reports. We also do not see Xehanort brandish his Keyblade very often. In fact, he only visibly does so in the presence of those who respect the Keyblade's power (i.e. Braig, TAV, Vanitas, etc.). It is entirely possible that, if Xehanort CAN control Ethereal Blades, he would do so readily to double his attack potency. Two hands, if used properly, are always better than one.
2b. Two definitions of Ethereal, the descriptive adjective, include "Spiritual" and "Composed of Ether/ Aether". Many Dark powers seem to be of Aetherial origin. (I do not know how to make the weird A:E fused letter in this forum)
3.Considering that Nobodies come into existence in the World of Darkness, (based off of Secret Ansem Reports in KH2), it would explain what happened to Xehanort's body after his heart was released to enter Terra's body. Seeing as how Xehanort and Eraqus both had their bodies "disappear" when their hearts were released, and they both released their hearts into Terra rather than simply being destroyed, I believe Eraqus and Xehanort could potentially both have Nobodies that appeared in the World of Darkness.
3a. Yes, I am implying that I considered that Eraqus' Nobody could have been the Mysterious Figure/Unknown. It seemed plausible when you consider that Aqua kept Eraqus Keyblade in the World of Darkness, thus disabling his Nobody's ability to use it. It similarly seemed plausible if you believe that all of the TAV fights with Mysterious Figure are Canon. I have discounted this theory purely because of a photograph pertaining to BBS:FM. In Final Mix, there appears to be a new Secret Boss that wears Samurai-esque armor and uses Eraqus' Keyblade. Disregarding that information, yes, the Eraqus Nobody Theory is still plausible because A: the blue Ethereal Blades may relate to a person using them if they control Light more readily than darkness, and B: Eraqus' Nobody would be unable to use the Keyblade Aqua is using.
3b. The fact that the Land of Departure becomes Castle Oblivion implies a close nature between the Land of Departure at the time Aqua fights (canonically for this theory, but can still be the time of fight for the game) Mysterious Figure, and the World of Darkness. Because Castle Oblivion lies in the World Between Worlds, it would be easy for a Nobody to appear there before any other place, especially knowing that Nobodies come into existence in the World of Darkness.
4. Throwing together 1+2+3, The Mysterious Figure wields Ethereal Blades rather than a Keyblade, just like Xemnas. Xemnas obviously is linked to Terra/Xehanort for obvious reasons. The latent ability to wield Ethereal Blades could be a "Pseudo-Muscle Memory" of Xehanort's, considering the time his Heart spent in Terra's body. If assuming 2 is correct, then Xehanort would know how to control Ethereal Blades through control of Darkness, and thus his Nobody would as well. (Remember, Roxas is the only Nobody we have seen that has no memory of his true self's past. If Xehanort used Ethereal Blades, his Nobody could too). Additionally, the potential timing of the Aqua fight adds up, as does the reasoning behind wielding Ethereal Blades rather than a Keyblade. Lastly, the location of the Mysterious Figure fight accounts for the connection that Nobodies have to the two Worlds and the space between.
Just my two cents. Take it for what you will. And if my theory is proved wrong in future KH installments, all you House fans can take my logistical addition and tell me "you were at least 6 wronger".
Cheers
