Everyone likes to second guess the direction of a scifi show - but only when the scifi show has some logical structure to it. A lot of BSG must be taken on faith that everything the writers will go somewhere with it, but unlike shows such as LOST, you can actually see things evolving logically.
So, given that BSG has hit the sweet spot - here's my prediction for Season 3. The fleet will find Earth, yes indeedy. The Cylons have already told Starbuck that they will find Earth. The problem is, everything has happened before.
When they stood upon the map to Earth on Kobol, did any one else notice that it was more of a memorial than anything else? My guess is that the year will not be 2006/2007 when they arrive at Earth, but something more along the lines of 8006/8007. The book of gythia talks over the Kobol events taking place 3000 years ago or some such? So if we say everything has happened before in a nice neat cycle, then humanity had to leave Earth.
Our meager technology gave us one planet to go to - a planet that is very much like Earth, Kobol. We went there, we settled, we pined about the days when we were back on Earth. The symbols of our sky became something more than legend, as we are now a space faring race.. they became our gods once more as they had once been back on Earth.
But, as we always do, we screw things up. Bit by bit Kobol became a not-so-great place to live. So we left, but this time we had more options, more ships.. we went to the twelve colonies. Earth is long since forgotten, the books are wrong about the 13th colony - it was the 1st, at least, the first as far back as any one can place it.
We like to conjecture even today that Humanity may have come from the stars, or from mars, or from anywhere but our own planet. We're always looking for "the missing link". Well BSG is suggesting the missing link is another species desire to be human. Taking that 'next big step'. From cavemen to human, from human to cylon.
The humanoid Cylons are flawed - they have inherited all of our bad traits, yet accuse us of them. Some of them have realised there is more to humanity than our primeval flaws, such as love. A final battle will take place between Humanity and the enlightened Cylons and the Cylons who believe they are superior. This will happen around Season 4-ish. And what's more - the Human/Cylon unity will win. They have more to live for than the regular Cylons.
And so, once the epic battle has concluded, we will not hear anymore of BSG.. the remaining enlightened Cylons and humans will settle on a new planet, beginning a new era of 'Humanity' in which the language of the machine and the language of humanity are combined in one.
The real question remaining is - when will Baltar test himself with his Cylon detector and discover that he is in fact a Cylon?