Well for me this has rarely happened but I can think of at least 2.
The first is in Christopher Nolan's Batman films and "The Dark Knight" was SO much better than "Batman Begins"!!! :D I've always liked Batman my whole life and watched the 60s show & film, the 80s/90s films, and the cartoons including the Justice League ones. I've always just loved Batman/Bruce and he still is my fav superhero!!! :D But when it comes to Nolan's trilogy, I think so far "The Dark Knight" was just fantastic!!! :D SO well written and directed by Nolan (who is a genius and I LOVED "Inception" too) and acted!!! :D We'll see what Nolan's 3rd and final Batman film "The Dark Knight Rises" is like next year, because it could possibly be better than the first 2. ;)
Then the other that stands out to me in comedy is the 2nd Austin Powers film. :) It actually was the film I saw first and I watched the 1st one after it. I just thought the 2nd one was more funny and better written and we had Mini-me!!! :D The 3rd I didn't think was good, but for me the 2nd one is the best. ;)