Yeah yeah, I know this is like two years old but since this topic recently popped up in the KH3 section there's a detail that I'd like to add to debunk your theory. (sorry)
for one, I believe that you've misunderstood that final battle between Ventus and Vanitus at the end of BBS. They didn't reunite in the end. Hell no, if that happened then the X blade would have been completely forged and all hell would break loose. Ventus destroyed Vanitus along with the X blade. Because of this, his heart broke since he destroyed his dark side and the X blade which also had fragments of Ven's light within it. So with that evidence, it can be seen that Vanitus is gone and has been such for a long while. And that evidence in itself keeps Vanitus from ever coming in contact with Sora's heart. Sure there was the connection with the appearance but that was only because of the sync that him and Ventus's hearts had. Sure that short cameo in DDD would seem to be disproving of my evidence, but that was, as Nomura said, Ventus's reaction to Xehanort's darkness and making a hypothetical connection to his long gone dark self.
and another point you've seem to misunderstand is what you said here about the reason Vanitas looks like Sora:
"However its far more complicated then that. Lets start at the very beginning of Vanitas's birth. He was getting sucked out of Ventus when Sora's newborn heart floated in and interacted with the two of them, healing Ventus and (my belief anyway) giving some of Sora's darkness in his stronger heart to Vanitas and thus making his appearance the dominant one even though he was supposed to be made from Ventus.
So this mean Vanitas and Sora were born at the same time even though one was full grown and one was a newborn baby. It also means that if I'm right That Sora was not entirely whole when he was born, meaning he was missing a lot of the darkness in his heart which may explain why he is so happy all the time. So in a sense Sora and to a lesser extent Ventus were the light half and Vanitas was the dark half of two hearts. "
Vanitas was born when Xehanort separated Ven's darkness from his light right? But you're saying that while that was occurring, Sora's newborn heart randomly was floating around in the Keyblade Graveyard and interacted with Ven and Vanitus. That doesn't make any sense at all. For one, I could go as far as to say that Sora wasn't even born yet. But I have no access to Sora's technical birthdate in the timeline so I'll just throw out there that Destiny Islands, and the Keyblade Graveyard are two completely separate worlds. Sora's heart, even as young and rambunctious as it was, would have no reason to go out wandering between worlds for some vague reason.
Oh and to add an extra detail, the reason why Sora is so happy go lucky remains the reason that was stated in DDD's ending: because he embraced the childlike innocence of the heart and kept that with him even as he grew up.
Let me explain the actual process here.
Xehanort vacuums out Ven's darkness and that darkness becomes a sentient independent being of pure darkness. Because everyone's heart has a dark side, Ven basically loses half of his heart and his heart is literally 'broken'. Xehanort drags Ven alongside him to different worlds etc until one night for some reason that hasn't been explained yet, Xehanort leaves Ven's body lying on a palm tree on the destiny Islands for a short time. During that time is when Sora first interacts with Ven's heart. Ven borrows some of Sora's light, thanks him and then awakens with his heart, now of pure light, restored. So I guess we can call him a PRINCESS OF HEART NOW EH?
Now allow me to explain what happened in between the lines. (I'm sorry, I'm not sure if this is canon, but I remember reading something in an interview and discussed this with a friend and we agreed that it was canon)
The case of Vanitas is a bit similar to Xion's. When Vanitas was first born, he has no face similar to Xion when she was first created. (Or maybe he had a face that was totally different or something we probably won't know unless it's in an interview I haven't read yet whatever it isn't important.) Ven and Vanitas clearly have a connection even when they're separated. They're halves of a whole and because this is Kingdom Hearts that is a pretty solid connection. Ven takes in a part of Sora's light. So now Ven has a part of Sora within his heart. This in turn because of Vanitas's connection with Ven causes Vanitas's face to change into a Sonic OC like re-palette of Sora's older face. Why older face? Because Ven is a teen after all. Like I said before, the situation is similar to Xion's. They both start out with no faces, and then via a connection (the connection between Van and Ven/Xion interacting with Roxas and Roxas being Sora's nobody) they gain a face. You get my point here?
(Though I find it as an amazing coincidence that both Vanitas and Xion both have black hair)
And another point to mention, what evidence do you have to support that Ventus lost his memories after his fight with his dark side? The reason he's in a comatose state is because his heart is broken (again). I understand if you give me evidence that Roxas had Ven's heart within him but didn't have Ven's memories but I think that it's pretty solid that (not technically canon yet) that Ven's heart was lying dormant within Roxas. Memories included.
All in all, your theory was quite developed and I applaud you for such a theory. It's just that sadly the foundations of that theory were flawed.