I was chatting with someone at my work who is a BSG fan and they brought up an interesting idea. I'll doubt it, personally, but it would be an interesting turn and definitely one worth talking about.
What if the fifth Cylon was the President of the Twelve Colonies? I forgot his name but he had a scene in the episode where it is discovered that Laura Rosalyn had a relationship with him. Having a Cylon as the leader of the Twelve Colonies would have also ensured that Baltar would have been chosen to create the new navigation program. He would have been a key figure in ensuring the total and quick collapse of the government.