Here's my take. Besides the Zombie combo, all the villains in Shippuden pretty much blow away the subs. I see dubbed and subbed Konan as pretty much equal.
Troy Baker and Neil Kaplan have amazing voices and definitely capture the evil nature of Madara and Pain. I'm torn on which Madara voice is better though. The sub is growing on me. Sakura's voice is awful. Sasuke is meh. Naruto's sub voice wins just because the actor has so much better of a feel for Naruto than the dub VA. Hinata does a good job I think capturing the Japanese feel.
I LOVE Shikaku's subbed voice. Probably my favorite. BTW, does anybody know who's going to voice adult Obito? I've heard it will be Vic.