Don't keep secrets when "It's the Characters, Stupid"
Moore famously declared, when composing the end of the BSG story, that "It's the Characters, Stupid." He wanted to focus on what happened to the characters and their story, and the plot and mysteries took second place.
I can understand that philosophy in writing. However, I do believe that if this was truly the case, the right thing to do is not create giant mysteries for the audience.
Some of the best stories out there have revealed their ending early on. (Some are even non-fiction so you know the ending in advance anyway.) With the ending known, the story becomes about how we got there, rather than wondering where we are going. As such the story moves its focus to characters and away from big mysteries.
If this story was to be about how Hera became mitochondrial Eve (and in the end, that was the root of all the elements of the closing) then the best thing to do would have been to reveal that right up front. Play out that scene in New York with Ron Moore getting the inspiration for the story early on. Show the ancient Earth as being out there. (They did show us Earth at the end of season 3, but it was modern Earth due to poor communication with the graphics dept.)
Or, if you want to have the shock of finding ruined 13th colony Earth, reveal the truth after that.
The show had lots of big mysteries. Many people enjoyed it for these mysteries, but if the show is really about the characters, the mysteries were a mistake. And we still would have puzzled over them. Fans would have spent hours discussing just how they get to Earth, and just why there is no record of them, and how they could possibly have interbred and other things. While watching the characters have their journey.
It becomes clear that the whole ending is just there for the Eve plot. All the controversial parts of the ending, the ones that make no sense, are driven by it.
- We currently date Mitochondrial Eve at 150,000 years ago. So that is when they arrive. 50,000 years ago (Great Leap Forward) makes far more sense otherwise.
- For this to be true, they have to have been able to interbreed with the natives. And so the ridiculous ability to do so, explained as a miracle from god.
- To have no record of their arrival they have to have discarded all their technology and ships. I haven't read any critic who thinks this story was credible.
- To have no record of their culture, it also had to vanish, which means they mostly got wiped out.
All these things that we fans have complained about are driven by this one cute little trick, "Hera is a sort of Eve." Sadly, alien Eve is one of the more clichéd story lines of golden age SF. Editors even got tired of it. Moore gave it a twist, the synthetic (God and Kobolians together) Eve arriving and breeding with the natives, but it's still a pretty poor, and unoriginal plot twist. It doesn't justify having to tear apart so much that was good in the show.