Having now seen the end of Season 3 SPOILERS ALERT I'm not more comfortable giving my idea of what will happen in BSG. If they play their cards right.. Battlestar Galactica ends in Season 4. If they try to continue it beyond that.. then they're idiots.
So what happened all those millenia ago that made the prophecies possible? As we know, Humanity started on Earth. The people from the colonies do not know this - they believe they came from Cobolt. However, Cobolt was too unpopulated, too few structures to support this idea. There was no developed society on there struggling to break away from their planet like there is on Earth today. Cobolt was less developed than the various colonies for that matter.
No, I posit the theory that instead, humanity came from Earth and travelled to Cobolt. Somewhere along the line humanity evolved and became.. sort of.. god like. In touch with the universe, the stars, they could do anything and go anywhere. They spawned forth their children in to the stars to colonise.
When the Battlestar Galactica and Cylon fleet finally arrive at Earth, they will find a the source.. of themselves and everything that goes on in their heads. The source of their prophecies, the source of their dreams and destinies. They will all discover that they are all connected. And the closer the two fleets get to Earth, the more things will start to "switch on" inside them.
The Cylons used human DNA and adapted it - they too are children of Earth, so the group will grow together until they realise the stupidity of their past and accept their new future, as part of a unified whole. Earth didn't just colonise Cobolt - they spread out to the stars in all directions and the same thing happened every time.. humanity and machine merged to create a superior race that merged back in to the greater whole when it finally returned to Earth.