That Mana was "with" Nea up until the end means nothing if Mana and the Earl occupy the same body. xD
Maybe if I explain more, you'll see what I mean. If you agree or not after that is up to you.
1. The way those of us who believe the Mana = Earl theory see it is that Mana 35 years ago was just like Allen is right now: struggling to keep the Noah memory *away* and stay a regular human.
2. Nea and Mana tried to run away from the other Noah clan members, but as we've been seeing with Allen, it's impossible for a Noah to hide from the other Noah... so Nea had to fight to protect Mana. Unfortunately, despite all that, the Earl gained enough control to finally kill Nea.
3. Obviously Mana came back after Nea died, but remember what Cross said? Mana was never the same after his brother died and had probably gone insane. Could it be that Mana lost control, let the Earl kill his (mother and) brother, and is so wracked with guilt (Allen's hallucination of Mana from Nea's memory in 212: "Do you hate me?" AND 218; Earl hallucinates Mana saying "Nea... I am sorry, Nea..."). What did we just see in chapter 218? The Earl is insane too! Coincidence yes, but there are a *LOT* of these "coincidences" going on. What did we see in chapter 187 (and then again at least one more time during the NA Incident)? The Earl has a fond memory of, and feelings for, Nea that resemble Mana's likely feelings about his younger brother. (The Earl even *calls* the 14th his brother at at least one point-- I personally think that's out of his *confusion* rather than it having to do with them both being Noahs.) *Looks* like Hoshino could be giving signs that Mana is still fighting back from deep within the Earl's mind.
Here are some subtle yet compelling hints:
a) In chapter 205, Road said Nea "fought for Mana."
b) and that's after quoting his last words for Mana
See both here:
http://www.mangahere.com/manga/d_gray_man/c205/26.html
http://www.mangahere.com/manga/d_gray_man/c205/27.html
"But it's a secret," she says before disappearing. So what's the secret? Maybe it's the same thing to do with the 14th that she told Wisely to shut up about in chapter 187, because it's a "private matter." :>
It could also be what Road and the Earl are talking about where they first appear in chapter 188:
http://img1.d-gray-man.com/image.php?id=188&what=18
http://img1.d-gray-man.com/image.php?id=188&what=19
Now check out what the Earl says just two pages later):
http://www.d-gray-man.com/manga/image.php?id=188&what=21
"I as the Millennium Earl can't stop..." and "I can't allow myself to stop, no matter what."
Sound familiar?! Remember, what Road said in 205? These were Nea's *last words* and they were for *Mana.*
(**Note: Most sites have that translation that says he must "keep standing," which makes no sense in context, regardless of whether you believe this theory or not. I think that's gotten people very confused...**)
These sorts of subtle hints, once you start to notice them, are everywhere!
4. In chapter 214, Nea says he'll keep his promise to Mana. We think Nea promised that if Mana became the Earl for good, he would kill him (like Kanda intends to do if Allen "permanently" becomes Nea, though we know that won't likely happen) and become the new Earl (which Nea says he's going to do in chapter 188, I believe).
So to us, these "secret" words, and the rest of the "private matter" between the Earl and the 14th is looking more and more like the Earl = Mana, and Nea chose to take Mana's side instead of joining the Earl. We think because he's clearly gone quite insane-- probably from the grief over killing his own brother-- the Earl's mind is just too *scrambled* to remember things clearly, much like Allen's too scrambled to remember 35 years ago, much to the 14th's chagrin.
****
BTW I may have spoken too soon about the twins being one person (in the present)! You may be right about that one. Except I think that what it might be, as others I've discussed it with think, is that 7000 years ago they *were* two people, but every time they reincarnated, they were born from a single regular human. So ORIGINALLY they were two people, but because their Noah power is shared, they always *reincarnate from one person.* I still think the picture should have matched the text then, but whatever. :D