Cavil's Evil Plan rewrites the whole show
The newly revealed plot, with Cavil as the cause of so many of the events in the show, but some other hidden being (the sender of the Messengers) with a secret agenda, rewrites a lot of the show. In some cases it does so retroactively, as they had not written the Final Five plot until the end of season two. But let's consider:
One question needs a bigger answer. Do the new humanoid Cylons have the uploaded memories of Centurions? Clues are contradictory. We are told the Centurions negotiated peace in exchange for biotech. Surely they didn't just want these new alien Cylons to create their own children and call them successors to the Centurions? Yet we see no sign of memory of metal form, other than Cavil's claim that "the humans enslaved us." In the other direction, we are told that Ellen raised John like a young boy, and so were all of them raised, though in a short period of time. So was he a baby or already a thinking mind?
John hates all things human. He hates it because he feels trapped in a human body, when he would prefer a metal one. He hates his creators for putting him in one. But if he was the first, and he was once metal, wasn't he the one begging for the humanoid body? Is this all his regret over this?
The Centurions invented monotheism and a loving god, and converted Ellen. Why is the first new Cylon an atheist?
We need the answer to this question because it tells us a lot about motives, and John's motives are now the driver of most of the story. His hatred for the human form that was forced upon him leads him to drive the genocide, it leads him to torture his creators.
The Cylons wipe out humanity because they believe it is God's will, and that they must kill their parents before they can thrive, and in retaliation for years of slavery. Or so they believe. But in fact, the humans are not their parents. Their memories of their parents have been wiped by John. Their views of god, presumably given them by the converted Final Five, are perverted. They don't have any reason to wipe out humanity, John invents one for them. They do it with aplomb, so they are perhaps not entirely innocent, but it seems that there is now just one being to be blamed for the genocide.
John wanted to give his creators "a front row seat to a holocaust." But, in spite of many opportunities to kill them, he clearly doesn't want to do that. He wants to show them how bad humanity is. He makes them bad humans, gives them flaws they may not had previously had.
This means the escape of Galactica, with Tigh and Tyrol on board, and Foster nearby in Colonial One, is Cavil's plan. Further, he goes and picks up Ellen on the planet and dumps her with the fleet. Anders gets to run a resistance but later gets to the fleet in spite of impossible odds.
(According to the writers, this orchestrated escape scenario was not in their plans but makes sense in the current context.)
There is no chase. Cavil always knows where the fleet is. His resurrection equipment is getting regular updates from the Final Five and others on board. The "find" the fleet when they feel like it, but in spite of overwhelming military superiority, never really hurt it. But they can find it when they need to. When D'Anna wants to deliver a documentary, a raider "finds" the fleet to pick up the transmission. When Bulldog needs to be chased to the fleet, he finds it. (Though there is an off-screen explanation for that.) When the fleet is going to the Ionian Nebula, they keep following it. Six suggests it's a ship with a radiation leak, which they send out on a decoy mission, and they still find the fleet anyway. In 33, the first episode, they keep finding the fleet and stop when the Olympic Carrier is missing and then destroyed, but is this really how they did it?
They must always be close, so that Cylons on board can download, and so that the Final Five can download when they finally are killed Cavil won't miss that, this is all about proving something to his creators.
Cavil seems to be the one gunning to destroy the fleet at times. But if he destroys humanity, he can't show his creators how bad it is any more. His real agenda is not to do this.
Only one thing takes priority over teaching a lesson to his creators. His fellow Cylons must not discover what he has done. He has enslaved the Centurions, he has hidden the Final Five. The idea of #3 seeking the Final Five makes him take drastic steps. The freeing of the Centurions makes him kill half of his fellows.
This is new, of course, but just what was it about Daniel that drove John to want to wipe him out? Can it simply be that as a "sensitive artist" he was too human, among the Cylons, and thus had to die? Or is it something more than that? For example, many peg Daniel as Starbuck's father. If Daniel could easily breed, this might make Cavil fear him, because he has heard the story of his creator's planet, where Cylons decided to live as breeders and even gave up their resurrection technology because of it. This would be a nightmare to him, worth stamping out. If that's the case he should have been wanting rid of the Cylon breeding projects and Hera most of all.
You may think I'm getting overly critical about scientific accuracy, but here I will criticise the basic story of good and evil inside this show. I think it's wrong to concentrate all the evil in one character. I liked the idea that the Final Five had a hidden agenda, and some responsibility for things going wrong, resulting in genocide. I felt they had to at least know the war was coming, accepting it as part of the cycle. But no, they were just prisoners. Their only error was making John and not realizing how dangerous he was. The other Cylons had all the good upbringing they had from the well-intended Five removed, and became machines ready for genocide.
Evil isn't that simple. Evil should not be concentrated into one super-evil character. I find that plot inferior to other stories of evil, that try to explain how people come to make evil decisions. "Not liking being stuck in a human body so destroying humanity" is not an evil plot I can identify with.
The Temple of Five, and other things
Ellen says they visited the Temple of Hopes but did not modify it to show their faces. Their visit would have been around 300 to 500 years prior to the show's events, based on my guess as to the distance from Kobol to the colonies. At any point, it's long after the 12 tribes fled Kobol.
But the 12 tribes have scrolls talking about a famous lost "Temple of the five priests who worshiped a God whose name cannot be...(spoken)" This legend comes from before the Final Five were even born. So they are not those five priests at all.
In fact, the Final Five were not special until 40 years ago, when they birthed the other 8. Their role in galactic history was minor. They were five survivors of a war on a slow boat to Caprica. The only thing special about them was that they had received "Messengers" (what RDM now calls virtual beings) to warn about the war. And they might be the last 5 Cylons at the time, though we can't really be sure. Point is there is no reason to make an elaborate temple to show their faces until there are 8 Cylons who might find this important.
So it seems that the other string-puller, this god, modified the temple quite recently. And it may also be the case that the Tomb of Athena, while it exists in ancient legends (just like the Temple of Five) is also a recent modification. What else is a recent modification?
Why does he unbox D'Anna? He already knows what she knows. He tells her it is so that she can negotiate peace. But how can he do that? He can't let her tell the others what she knows, have them find the Final Five, for then his game could be up and he will be destroyed. Since this unboxing was written after they had worked out the Cavil plot, this remains curious.