The funny part is how Stubbs has had an awesome OBP (.375) since Votto has been out of the lineup. For the year he's also got a .324 OBP in the 2 spot, which isn't fantastic, but it's good enough considering the fact that his speed is most valuable in front of Votto (distracting pitchers, getting in scoring position). I say, all things considered, leave him there.
The biggest problem has been, and remains, the leadoff spot. Without question, that needs to change - we should try BP or Paul as you suggested, or even Hanigan. I like Cozart a lot but he is not getting on base enough to lead off, and Dusty can't use speed as an excuse to keep him there.