I definitely agree with you on this one. While it had its weak spots, overall I really enjoyed the film. I was disappointed to see it get some negative reviews from some of the major geek sites who seemed to want to nitpick it apart for no reason. The weakest part of the film for me was definitely the fight on top of the train, mostly because it seemed to never end. But I'd gladly sit through scenes like that just to get more Yukio action.
I think the glut of superhero films have kind of changed expectations. After Dark Knight Rises, Avengers, and Man of Steel it seems everything is SO big. Even Iron Man 3, which was also a bit of a more personal story about Tony still had the president in peril plot. The Wolverine has very little in world-shattering stakes, and I wonder if that puts some people off. No saving the world from alien invasion or even a nuke, just a man dealing with the demons of his past. Sure there's action, but the action served the story and not the other way around, and I wonder if some people don't go to these movies for that sort of story.