I loved the Nagasaki scenes. In fact, I thought they were best use of the 3D (which the movie didn't really need otherwise). I loved that shot from the bottom of the well, where you could see how Logan was holding himself up by his claws at the top of the well. That was an amazing shot.
But yeah, I agree...seeing him vulnerable was one of the best parts of the movie. He really had no idea how process that. I loved Mariko's answer at the vet's office, when he said he'd never need 'this' before, and she said, "Help?". That was great. He was supposed to be rescuing her, but wound up needing her to rescue him.