The Earth reveal solidifies my suspicions on the Head Crew and what's going on.
Warning: long and stupid, my moment to geek out in geeky speculation for the week. So, okay.
The thing is, what I wonder, is if the Head Crew is not all evil. So far, I think that Head Six and Head Baltar are likely the official bad guys here, and their appearance and personalities are designed to manipulate the specific weaknesses of Six and Baltar.
However, despite my suspicion about Kara's Special Destiny (tm) (see below) I somehow, for the moment, do not feel that Head Leoben is evil. I also do not feel, for the moment, that Head Eiosha is evil.
Kara's Special Destiny (tm): I think what we could be looking at here, is that Kara's destiny is a dark one. The prophesy about her "leading them to their destruction" could be simple and direct. Kara could be the unlucky person chosen on this cycle ("all this has happened before...") to be the Pied Piper, who helps the evil Head Crew members in luring humanity to its destruction.
My overall suspicion about what is happening so far:
The Head Crew could be some form of ascended intelligence ("Paging Dr. Jackson...") that very well might be human in origin. Or, Moore could pull a fast one and make the Head Crew a truly alien force - perhaps as a "realistic" way to handle aliens, the aliens are so abstract and of a different order of existence that they will never be perceived directly by humanity. However, a possible scenario... the Head Crew are representatives of a force or civilization that wishes to either destroy, hamper, or severely guide through artificial Darwinian selection, what we would recognize as regular humanity. Before dealing with Earth, let's work backwards from Kobol.
Kobol's legends say that humanity lived under the rule of the "gods", until something happened to expell them from paradise. Most of humanity left and went to the 12 Colonies. A small group however, did not board "the galleon" and instead went into the mountains to the tomb of Athena. It almost seems suggested that it was these people who could have left for "Earth" and been considered the 13th tribe. But why did they not follow the others to the colonies?
Let us say that the Lords of Kobol were in fact, the same entities behind the Head People. And that Kobol was an attempt to guide and shape humanity along particular lines. But that did not work out. Something went wrong. The humans of Kobol became corrupted against the influence of the Lords. Therefore, they were "expelled". The galleon was constructed, perhaps as a display of "mercy" by the gods, and humanity was told to leave. This was in fact an attempt to salvage the plans of the Lords. They would allow humanity to go "free" but under careful observation, to grow again, sort itself out, create a fresh round of diversity, before the Lords or Head People would interfere directly again.
Some however, refused, perhaps out of random stubbornness or maybe because there was another force. Perhaps one of the Head People playing Lords of Kobol did not agree with the others. They might have chosen to save the humans who would listen, and try to help them escape, sending them in a pilgrimage back to humanity's original (or maybe, merely previous?) home - Earth. So, a group of humans, or whatever it was that was on Kobol under the rule of the Lords, left to find Earth anew, and along the way, left markers of their passing such as the Temple of the Five.
What happens next, is that the mysterious Head beings or whoever, watch the Colonies for thousands of years, until they decide to "kick over the ant hill" and try again to use humanity. There are a few possibilities (that again, all relate back to Earth that we now have revealed to us).
Perhaps the Cylons are in some way, the physical agents or enforces of the Head Beings. The creation of the new generation of mechanical Cylons could, originally, have been influenced by the Head Crew, and the original Cylon rebellion could have been secretly programmed into them from the start. Perhaps the Cylons were, originally, meant to drive humanity to the brink of destruction, at which point the Lords would take those who survived to be their experiment - to create the next Kobol-like society. But humanity had grown too strong, and the Cylons were at a stalemate. After the Cylons agreed to retreat, they needed to be shown the way by their true creators. Therefore, the wandering Centurions are contacted by "God", a representative of the Head Crew who has the job of managing them. The Cylons are upgraded. Clearly, a new level is required, and it may be something pulled from the past - prior advanced versions of Cylons.
The skinjobs are created. The resurrection system is put in place - not actually built by the Cylons themselves. Perhaps much of their technology, such as advanced jump systems, does in fact come from the Head Crew. These new Cylons are indoctrinated that they must follow the will of their very own Cylon god, and are sent off to do a better job of destroying human civilization - and they do it well.
But, the spanner in the wrench, is that not all of the Head Crew are of one mind. There are dissenters. They have different intentions. How do the Final Five fit in?
Remember, if Earth was destroyed thousands of years ago, and humanity left - or was guided to - Kobol, that means the humans who returned to Earth found it in ruins themselves. What did they do with themselves for thousands of years, as Colonial civilization developed? Perhaps they were meant to discover and work out the truth of the whole rigged system. One possibility is that the humans of the 13th tribe chose not to stay on Earth or rebuild it, only to learn from it. They evolved themselves, and after thousands of years, have become advanced and powerful, and perhaps allies of the "good" members of the Head Crew. Perhaps they created the type of Cylons the Final Five are, or they /became/ the type of Cylons the Final Five are. Perhaps the Five are themselves representatives of the good-guy Head beings, who helped the 13th Tribe. (More on that in a moment, relating to Earth itself...)
So, the Final Five returned to the Colonies to infiltrate them and fight against the influence of the Head Crew. The skinjob technology being developed at that time was in fact, a cruder version of what the Five were. It's possible that the blocks programmed into the skinjobs about thinking who the Five are were put in place to prevent the Five from directly recruiting the skinjobs to their side. But wait - why do the Significant Seven know to consider the Final Five to be models of Cylon at all? Why not block every element of their existence if the Five are a threat? Perhaps the 12 humanoid Cylon models are in fact an old thing, that the Lords of Kobol / Head Crew merely pulled technology from for their plans. However, the Seven could be intentionally inferior versions of the "true" Cylon beings. They can't reproduce on purpose, to help control them. Perhaps in their ideal state, they'd be like the Five.
So, what about Earth?
A possibility: at some point, Earth creates the technology for artificial life, or, the Cylons. It goes through stages, starting with toasters, and graduating to supremely refined models that the Five represent - but originally there were 12. Something happens there. Perhaps the Cylons are corrupted and used against humanity. Perhaps the Head Crew are an even further evolution of intelligence, created from humanity or Cylons. Or perhaps they're an alien intelligence that came across humanity and decided to mess with it. But, Earth is destroyed, and fleeing humanity are guided to Kobol, to become the subjects of the "lords" of Kobol, attempting to create a certain kind of society. Hell, maybe the 12 refined humanlike Cylons WERE the Lords of Kobol originally. Perhaps each of them was the envoy from the higher power to the people. Perhaps the Five were those who rebelled and took the 13th Tribe back to Earth. This would make an elegant circle, maybe, where the new generation of skinjobs (the Seven) are almost mockeries of the original Seven who stayed loyal to the Head people. More artificial, limited, crippled, mass produced.
As for where do things go from here...
I wonder if Head Leoben could have been trying to guide Kara through a pre-ordained "death" in a way that would undermine the plans for Kara? It sure seems as if Not Leoben was genuinely trying to help Kara get over her past, and come to terms with herself, and be at peace. If Kara is supposed to be the harbinger of death, would the Head Crew really want her to be at peace with herself? Could the original intent have been to have a broken Kara lead everyone to Earth? Could there be some advantage for the Forces of Gooder in having Kara be "better"? Could Kara yet do something to save the day? (Ye Gods, I know, it's Super Starbuck syndrome...) Perhaps the abilities given to Kara that allowed her to find Earth could be used by her in other ways. What if she can use this sixth sense to guide people away from Earth, and sniff out the way to the 13th Tribe, who might be real allies? Perhaps a messed up Kara would have gotten to Earth, and been too desolate to care or be a threat after seeing its destruction.
So, a final thought on The Plan.
Guiding the Colonials to Earth after the Cylon holocaust could have been the plan by the Evil Head Crew all along. Perhaps the "gods" would be revealed again in a new form to rescue dispirited, defeated humanity after having been shocked by the discovery of Earth, and presented as saviors... or A savior. Maybe that's the trick - this time, the Head Crew are trying monotheism. Or, maybe they're trying it... again. The Jesus Christ parallels with Baltar are perhaps more creepy if this is indeed all in our future. What if the insinuation is that our past has been through more cycles of all this? Perhaps the cause of humanity's turmoils and existing mythologies.
But, maybe now, all bets are off and it is anyone's game. The Five are here to mess up the Plan. There's a faction of rebel Cylons who are mucking things up real good. It would be something if the ultimate mis-direction of the series is that the real goal has never been getting to Earth, but understanding how Earth fits in to an even bigger picture. The words by Lee seem to carry some added significance - about how all this doesn't HAVE to happen again. While this is BSG and it is assumed everything will always have a dark twist or dark ending to it, I wonder if our ultimate ending might be more "happy" than we'd think. I'd almost wonder if a "war with the gods" is in the cards, here, for the big finish... or a battle to stop the cycle once and for all.
After all - there must be some way out of here, said the joker to the thief!