What are your mouse settings? Maybe using your configs I can finally figure out some decent controls.
I've played a few hours of Civ V with the default controller config, and it felt fine to me. There's some small things I would tweak, but it was completely usable. If you're having a lot of trouble with the default config, it may be something up with the hardware, or it could be that you're holding the controller wrong.
So, the way I hold the controller is fairly loosely in my fingers, so that the finger tips on my index fingers are resting on the triggers, and middle and ring fingers are curled around the grips just enough to use the paddles. My middle fingers are positioned in the curve where the grips end and the trigger begins, and the controller is partially resting on those fingers. The key, I think, is when you're holding the controller correctly, the face of the controller is pointed slightly up but mostly towards your body, as opposed to pointing towards the ceiling.
Holding the controller that way, you naturally manipulate the controls with the tips of you thumbs, and not the flats of your thumbs, which is very important for precise control on the touch pads.