The writer for BSG is actually very switched on. In his blog he has either pointed out reasonable counter arguments or actually admited they screwed up when people ask questions about the script.
The new BSG series is on a knife-edge for me right now as to whether it knocks B5 off the perch as my favourite sci-fi, or goes on the list of 'could have beens' like Nowhere Man and Lost.
I know the cylons have a plan. I remain unconvinced that the writer really has one though. The problem with an unplanned story is that there is no point obsessively re-watching episodes over and over again looking for hidden clues, because those clues aren't going to project more than half a season in advance. BSG has made a really good start at seeding clues, subtleties like most likely the war started because some twit accidentily or deliberately added the bible to their latest BIOS update. That this bible promises salvation only for the human race, so the cylon's never wanted to actually wipe them all out, but needed to find a way to 'convert' the human race into their religion (ie. make them lost, desperate, etc...) while also breeding their line into it so they can go to heaven too.
But it's about time for the cylons to screw up. If this series just keeps on going with this model of them being able to perfectly manipulate all human activity (eg "our baby will be born here") than the series will go stale. We need to see some notion of human spontaneity actually obviously thwart the cylon master plan, even if they recover and regain the upper hand. I don't care who's winning, but if one of them isn't even getting to play at all it's too boring for me.
Plus, desperation or not, there is no way I'm letting some guy who keeps talking to himself walk around unobserved on our only remaining battleship. I want to see Adama watching some of these security tapes right at the start of a scene before someone knocks on his door or something.