A few theories

****SPOILERS AHEAD****

Allen used to be friends with Nea and he was a bookman who became "involved" in such a forbidden way, he forgot everything about the bookman clan when Nea's memories got passed down to him. I can't find a reason as to why he would have de-aged or been born again but I would suppose it is because of some weird bookman antics or that thing about damaging Noah's memories

It seems Tickky betrayed Nea in the past as well, I'm not sure why road is always showing herself in her kid form but it has been mentioned that this is not her real form and that she does it because she likes it. Road says "Nea fought for Mana, but that's a secret" implying that Nea wants to become the millenium earl to save his brother and wants to become the pillar instead (maybe he wants to become another kind of pillar, one that is not going to destroy everything) although I don't understand why that would involve actually killing mana, maybe when the earl transforms into a pillar, the pillar just follows his will?. But Nea has said he hates humans so idk.

Why would apochryphos be following Mana? Shouldn't he have been more worried about the heart? He has said that the heart already knows who they are, and that they are just hiding away but inside the order if I recall correctly? This means we know who the heart might be and I think that Lenalee is simply a red hearring and that the heart is probably Jonnhy just that he himself forgot on purpose or something like that. Why else would he gain so much importance in the story if he isn't relevant in any other way?

Lavi's eye, or the bookman's eye is something that is only mentioned once but I think it's probably an "eye" that passes through generations, when you have it, you can record stuff that gets ingrained into it, much like timcampy's videos. That's why he lamented using it to find the key when they became trapped in the arc (because it wasn't an important moment).

I suppose a few Noah's have been trying to work with Nea to save Mana in some weird way but they can't unfollow the Earl rules or their Noah memories. Why would Mana be considered to be the Earl if Nea is also the Earls though.
It seems Noahs come from the modern world and even another dimension, Cross says "This isn't even your world" to Road and all uggh I wish I could just pick inside Joshino's brain