Its a retelling, as linx put it so well, its just like how DYRL? was a retelling of Macross and Girl In Gaea was for Escaflowne.
I think the OVA was more in-line to what Kawamori had in mind with the series. Aquarion minus all the "useless" episodes of the TV series and just concentrated with the "meat" you'll get the OVA.
You can still see the "tree hugging hippiness" of hory froating head in the OVA, but its done quite well with less cheese. Assault Type Aquarion gerwalk mode (Armageddon mode i think its officially called) gets more screen time.....awesomes!
There seems to be a switch in roles in terms reincarnations but i think its just to mislead the audience for now.
SPOILERS:
This was the strange bit in the TV series cuz they needed 3 people to pilot the Aquarion but in the TV series it seemed to imply only Apolonius and Cerianne were needed to pilot it 12,000 years ago. Guess they included Scorpius in as the 3rd pilot and the great betrayer of man-kind and to take on the role that Sirius was supposed to fill, since Sirius is already dead in the events of the OVA. Not sure if Silvia is really Scorpius or Cerianne for now but it seems to imply Silvia is Scorpius for now. Reika as one of the important reincarnations doesn't sit well with me. I never liked her from the TV series and neither now.