I think what they did with The Wolverine was great. They took definite influences from various comic story lines, including that original Wolverine run, mixed in a little bit of Old Man Logan, and did their own thing as well. It worked great. As a comic fan, like you said, I'll never go in wanting a 100% adaption of the comics, nods to the books here and there are great, but somethings work in the books that wouldn't really work on screen (like Wolverine's costumes).
The backlash against Iron Man 3's Mandarin is a good example. What they did was a ballsy fucking move, that NO ONE saw coming. How often do you get a genuine plot twist like that in films? But all the comic fanboys rioted and complained and now apparently they're shooting a Marvel One Shot that's "correcting" the Mandarin.