It's a tie between Nagato and Itachi for me.
Nagato because I very much enjoyed the action he brought to Shippuden. Kishi created a lot of suspense with him.
Itachi because I respect him for what he did for his younger brother. Saving his brother's life at the cost of his whole clan; who would have died along side himself and Sasuke if he hadn't done so. I feel this was a very tough decision for him, and I respect that. (I know it's just a manga but I liked it. xD)