Re: What didn't you like about the film?
Yashida didn't care if Logan learned martial arts. He wanted his healing factor. That was his entire motivation. He assumed Logan wanted to die (which he didn't), and thought he was giving him the "gift" of mortality. The whole point of suppressing his healing factor was so they could capture him and take it by force when wouldn't give it willingly.
Everyone who reads the comics knows Wolverine's connection with Japan, but that's never been established in the movie universe. Even the WWII stuff seen in Origins was from D-Day, so fans of the movies would have no idea he'd been to Japan (the Origins end credits scene was after he'd lost his memory, so any connection he still had was lost). So the idea with the film is to introduce both Logan and the audience to this new Japanese setting. And that worked.
The martial arts thing is cool, but it adds nothing new to the plot. We already know he can fight. The story was about Logan trying to reconcile who he already was, not try to become someone else.
"We're told we have to do what we're told, but surely...sometimes you have to be a little bit naughty."