It's been a while for me too, but from what I remember Caius's motives through the whole game was to save Yuel and break her cycle. He went to extreme means to do it, but it was all for her. After the regular ending where Noel and Serah put a stop to all that, the 'secret ending' implies that he actually just wanted to take over the world and be an evil bastard. That went against his characterization throughout the game. I could have interpreted it wrong.