I was going to make a thread for this, but after seeing the battle on Youtube a few more times, I'm beginning to think this is.. either MX's nobody or more likely, a new enemy. Let's go with MX's nobody first. Nomura said something was created or something along the lines of that, right? Honestly, I'm beginning to think that if MX had some sort of nobody counterpart, it might of surfaced in the Dark Realm. But wait.. how did it get to LoD? If you look at the background, it appears that this is LoD post-destruction, pre-Castle Oblivion (after Terra's visit, before Keyblade Graveyard). I think this puts it at the edge of the dark realm, much like CO was in the present timeline.
My belief for why it didn't completely disappear into the Dark Realm might have to do with it being an Inbetween realm, instead of being just another world in the Realm of Light. It's position might of allowed this being to reach it, though the being might of still been unable to go any further (without becoming more unstable than it already appeared to be), hence it might still be in the Dark Realm.. until it somehow gets released in future games (KH3 (or even 3D/ the final (hopefully) mystery game) and beyond)
Yeah, as for it being a new enemy, I can also see it being a survivor of the Keyblade War, trapped in the Dark Realm and slowly aging, if at all. Perhaps, he forged or nearly forged the X-blade to, but over time, he lost his ability to wield or might of been masking it when he or she fought Aqua. Who knows, maybe the darkness eventually destroyed (or almost did) their body, but they somehow found a cloak similar to Org. XIII's cloaks and that's why they kept on living. However, upon losing most or all of their body, they stopped aging and that's why they're still around.
I still can't explain the time thing though, but I feel that the fading in and out might also hint at an unstable being or at least more unstable, the closer they are to the Realm of Light. Perhaps, they still do have a body (but still somehow don't age or age VERY slowly), but it still can't keep its form, even in a world close enough to the Dark Realm to allow them to cross over. Honestly, I think it's more likely a new enemy though, who perhaps has time-bending abilities. They may start to surface in these last few games of the Xehanort sage, but won't be completely revealed until late in KH3 or even after KH3.
If it's his nobody, nobody-like counterpart, perhaps he will resurface entirely in KH3 and later find a means to rejoin his heart and maybe even find a means (via the time-bending stuff) to de-age MX into Sora's most powerful foe yet, Young MX. Imagine that, MX with all that knowledge, abilities, KEYBLADE, and young again, without Terra to counter him internally.