Wolverine vs Shingen is a much more powerful, emotional scene than the shallow, garish stuff with Viper and a guy in robot armor. There's probably no better example than the different climactic battle scenes. But all of the special effects-heavy parts and the loud, flashy action sequences suck and take away from the impact the movie would have otherwise had. The Wolverine and Mariko parts, basically. The good stuff, the stuff worth watching this for, are the slower, quieter parts of the story. But then you have this other stuff, far removed from that story, that seems to be studio-imposed and ultimately hurts what could have been one of the best comic book movies to date.
I know Hugh Jackman wanted this movie to be an adaptation of the classic Chris Claremont/Frank Miller comic book mini-series.