Now then, where was I? Spoilers ahead, peeps and peepesses.
Once we make the leap of logic and work under the theory that the Earth was wrecked quite some time ago, the immediate head-scratcher that presents itself is: why come here at all? Clearly someone or something wants the Colonials to get to Earth, as evidenced by what happened to Starbuck. But that same intelligence seemed very keen on making it as convoluted a process as possible. One possible explanation for this was to force the humans and the Cylons to work together, to discover Earth as a united front; although frankly it's a minor miracle that ever worked out.
Is this intelligence the Final Cylon? And if that's the case, did he/she stay behind when the Final Five travelled to Earth, or is there something more going on? We still have no idea how the skin-jobs were created. Ronald D Moore has already said that Tigh, Anders, Tyrol and Foster don't have model numbers (what happened to No 7? I've no idea, although even money says the question gets covered in one of the TV movies they're considering making after the series ends); which helps explain why there aren't multiple models, but more importantly it adds fuel to the idea that the Five may well not be part of the current generation of Cylons. They may have set up the current crop of skin-jobs themselves (Tigh points out that Cylon aging isn't impossible, not that it's inevitable). There are a lot of possible explanations as to why: one being the belief that they needed to procreate one way or another (note how this was passed on to their "children") another being that they needed a force capable of returning humanity to Earth (and if they figured could only do that by forcing another nuclear holocaust as a mirror image of the first, then it would betray a certain mechanical logic: they certainly know that it's worked once).
The corollary to this is the idea that the Final Cylon is a hangover from the original war. Again, I'm not the first person to suggest the Cylon "God" may actually be the only unknown model. Perhaps said model went through a similar epiphany to Caprica and (briefly) Boomer following the original war, and is attempting to make amends by bringing humanity home. The arrival of the fleet represents a plan that's been in motion for who knows how many millenia. For whatever reason (probably one of resources) the Final Cylon waited until the Colonials created their own race of Cylons before dispatching his four agents to help the toasters cyborg themselves the fuck up (it's hardly compelling evidence in the context of a sci-fi show about killer robots, but I always thought it was a bit of a leap from chrome-jobs to skin-jobs in just forty years).
All of this leads us to the next Big Question (TM) which is: what exactly is the fleet going to do now that it's "home"? More specifically, who are they going to fight? The current alliance with one half of the Cylons might still fall apart, of course (although that would undo a lot of interesting stuff that has been done this season, so I hope not) or the other half of the Cylon fleet could show up and start blasting at shit (certainly it would be interesting to see how the other three models respond to the the Final Five). Certainly things can't remain as they are, you can't spend ten episodes looking around the solar system and shrugging . But what if they don't go back to just slapping around the Colonial-made Cylons? What if they have to face a larger threat? Say, whatever happened to Cylon society after the first war. Just because the Final Cylon is interested in getting the humans home (assuming this isn't the mother of all traps, designed at finishing off humanity once and for all by wiping out 99.99975% of them on the colonies and then sending the rest of them into an ambush at Earth), it doesn't mean the rest of the first-gen bunch have to think the same way (if we go back to the cyclic time thing again, the Final Cylon might be analogous to Athena), which would allow the series to something new instead of constantly reshuffling the positions of the Colonials and the known models.
Anyway, that's all I got right now.
 This is another reason why I don't buy into the Colonials as Cylons idea; I'm far from sure it leaves any room for further development. We find out they're all skin-jobs and then... what?