New Genesis is supposed to give us a new and fresh experience, so as for me it's kinda dissapointing if Halpha is to be revealed as Naverius.
It could be true though given the similarities and all that you mentioned, but I prefer Halpha to be ... I dunno, something else .... may be a big mysterious mothership like the one in classic Phantasy Star III.
If PSCrew wanted the game to be a new and fresh experiance, they would of made it PSO3, PSU2 or at least a seperate game where SG and AC can be used interchangably.
But the fact you can start New Genesis with your old PSO2 character and how the meteorn are described it does sound like a continuation after a thousand years gap. Speaking of one-thousand years isn't it said that whenever the Profound Darkness is defeated it re-manifests after a millenium of rest, and given the Dark Falz may take form depending on various hosts it possess, it could be possible the dolls are the Dark Falz new form.
All in all, while PSCrew may say the game is suppose to be a new and fresh experiance, story-wise people will want to fill in the thousand-year gap.
I've yet to begin Episode 6 let alone know how it ends, but I pressume what happened is at some point it was decided for ARKS ops to be cryo'd and ejected into space, meanwhile what's left of ARKS, probably the inhabitants of ARKS Ships, decided to land on Naverius for colonization and renaming of the planet to Halpha. These various events have faded over history but probably due to orbital projectories the ARKS cryo-escape pods eventually returned to fall onto Halpha. Memory loss and atrophy over long stasis caused our hearty battle-hard operatives to practically start over as new "Meteorns".
Another thing I noticed, is they decided to name the planet Halpha, which could probably be a reference to the term "
The Alpha and the Omega" given Episode 5 was all about a world that, like Halpha, based and inspired from the history of Phantasy Star. Naverius could be regarded as the alt-universe equivilent to ESC-A Earth and given Omega picked Apprentices from both ARKS and Earth means there could be a sort of trinity between these three planets. So Naverius could be the alpha to the Omega and why the name Halpha.