A few spoilers ahead - nothing too bad, in my opinion, but I thought I should warn anyway.
To be honest, I have only seen the new series', starting with 2005, and I'm not really sure how to rank the three doctor's I've seen. I loved them all for different reasons.
And I agree about the writing having suffered ( The Vampire's of Venice? ), but I feel like they handled the Pandorica pretty well. They built to it subtly - not as subtly as Bad Wolf, and it wasn't handled quite as well, but still. I was glad to see how they incorporated some of the seemingly random episodes into the overall arch, like the Van Gogh one.
One of my problems with the newest season is how they threw some ideas around, but seem to have abandoned them. Like Amy not remembering the invasion of the Daleks. They hadn't been erased from existence, yet, so she SHOULD remember them, right? Unless I just misinterpreted something there...
And if you mean, by "female clone", the Doctor's daughter, I'm reasonably sure that they are not one in the same. It has been heavily implied that she is the Doctor's wife, and so that would be kind of creepy... to each their own, though, I guess....