How can we try to fit together a likely scenario for Zak?
Well, we need to understand the new BSG universe.
So let's start with Ron Moore's last universe, Star Trek: Deep Space Nine (DS9).
It had some elements that we see in BSG:
* religion plays an important role
* One is Chosen (the Emissary)
* prophecy is true (connected to hard-ish science by the fact that the ability to see the future comes from the wormhole aliens, who exist outside of time)
* interpersonal relationships are important
* "gods" are real (the Bajorans worship the wormhole aliens)
BSG is harder SF than DS9, but one fantasy element does remain:
* prophecy is true, and accessible to all persons (humans, cylons, human-cylon hybrids, and cylon ship Hybrids)
BSG also draws very heavily on Classic Greek and Roman mythology.
So a likely scenario is something like this:
Humans on Kobol built humanoid robots (call them Kobol Cylons) with some godlike characteristics (immortality), but human characteristics (much as the Classic gods like Zeus had supernatural powers but very natural appetites).
The Book tells us that humans and their gods lived together for a time on Kobol.
Then one guesses that something like most of the humans left to form the 12 colonies, and most of the Kobol Cylons left to form the 13th colony (Earth). There may have been some mixing (humans going to Earth, Kobol Cylons going to the 12 colonies - perhaps particularly as priests).
Now, say 40-50 years ago (or maybe longer), some catastrophe befalls Earth, maybe a war between various Kobol-Earth Cylons, or a war between K-E Cylons and K-E humans.
The Kobol-Earth Cylons decide to bring about a reunification of the Cylon and human races, in a sustainable peace. They locate the New Cylons (the 12 colonies Cylons) who have already developed Hybrids, and add the technology of resurrection, more bioengineering, and humanoid Cylons. As with the Kobol Cylons before, the humanoids are given human characteristics and failings:
* Brother Cavil as the New Cylon Zeus?
* Six as Aphrodite?
* Athena as... Athena?
(remember Athena is a huntress, as well as being wise)
Rather than teaching their New humanoid Cylons that they are gods, they teach them that there is a higher God, a God of love.
They send Kobol-Earth Cylon emissaries to watch and learn from the 12 colonies humans.
Perhaps one emissary is Kara Thrace's father? (Making her a Kobol-Earth Cylon - 12 colonies human hybrid.)
Then, by mistake? intentionally? 12 colonies humanity is wiped out.
And then we have the Great Experiment - can the New Cylons and the remaining 12 colonies humans learn to come to peace? Can they learn to love, because otherwise the humans will die, and the Cylons will be immortal but childless.
(Remember the Cylons Have a Plan - which may be the Great Experiment Plan, without the 7 known models even knowing about it.)
So Sam, President's Aide, the Chief and Tigh are all Kobol-Earth Cylons programmed with Deep Cover. As is/was Zak Adama. All placed in ideal positions to observe 12 colonies humanity.
Once they work their way towards peace, they will rejoin with Kobol-Earth Cylons (and any remaining Kobol-Earth humans, if there's any difference, and All Live Happily Ever After).
This addresses most of the mysteries of the show:
* Who are the Final Five Cylons and why are they different from the other 7?
- We know (from the ship Hybrid) that they come from Earth.
- Sam, President's Aide, the Chief (Galen Tyrol) and (Colonel Saul) Tigh are all Kobol-Earth humanoid Cylons programmed with deep cover who came to the 12 colonies starting 40-50 years ago
- Zak Adama is a Kobol-Earth Cylon programmed with deep cover who was ?replaced at birth? ?implanted in the womb? ?never actually seen born - Adama's wife knew?
* What's the deal with Kara Thrace and her rebirth and special destiny?
- Kara is probably a Kobol-Earth Cylon + 12 colonies Human hybrid
- she was probably resurrected by the Kobol-Earth Cylons, and her ship repaired / rebuilt as well by them (this means of course that at a minimum all Cylon-Human hybrids can also be immortal if they choose)
- she, along with Galen, were chosen/created to be key parts of guiding humanity & New Cylons back to Earth
* what's the deal with Roslin's visions, Kara's visions, shared visions with Roslin-Hera-Six, Hybrid vision, 12 colonies priest/prophet visions
- as I said before, in BSG prophecy is real, and any person (Cylon or human) can have prophetic visions
* What's the deal with Baltar/Jebus, particularly his visions of Six, and what's the deal with Caprica Six's visions of Baltar (which we only saw a few times)
- This is the only part that is not really clear. There are a few possible scenarios:
S1. Most likely: In the nuclear explosion that killed Caprica Six as she was holding Baltar, her upload got mixed in and crossed over with his brainwaves
S2. Baltar vision Six is an implant or some other technology used by the Kobol-Earth Cylons to guide Baltar, as part of their Plan (putting him roughly in the same class as Kara and Galen)
S3. Angel sent by God / Demon sent by Forces of Evil
S4. I think fairly unlikely: Angel / vision sent by Glowing Ship Gods (see original Battlestar)
(If it does end up being some Ship of Light literal deus ex machina I will be disappointed.)
I think that covers most of the mysteries.
* As in the First Hybrid and later Hybrid prophecy, Kara did lead the fleet to "the end of humanity" (in this case, both the literal end at destroyed Earth, as well as the figurative end, as the future of humanity is hybridizing with Cylons)
* The final five are from Earth as the Hybrid said, and the One Who Will Be Revealed (Zak) is not on the fleet, as Deanna said
* (Zak) Adama is a Cylon, as prophecised by Leoben
* The final five are different from the other 7 because they are Kobol-Earth Cylons, not New Cylons
* The Final Five Cylon that Deanna recognized and was sorry about was probably Tigh, and she felt sorry because #1 he'd spent 40 years fighting the Cylons and #2 they ripped out his eye and (maybe) #3 he killed his Cylon-collaborator wife
Anything I've missed?