While I won't be giving Megan Fox an Academy Award anytime soon, I wouldn't call her "bad" - her acting isn't "unbelievable" to me, and it doesn't take me out of the movie. As long as she stays in movies like Transformers or something where she doesn't need a lot of depth, I think that she's an appropriate actress for her roles.
One single "deus ex machina" doesn't ruin an entire movie.
Special effects are about the last thing that can ruin a movie. Does that mean that movies from the 80's and 90's that didn't have the technology we do now are all "bad" movies because their special effects suck?
The purpose of a movie is to entertain. Nothing else. If the movie doesn't entertain, then it is not good to those that it entertained. If the movie does entertain, then it is good to those that it entertained. Simple.
Yes, there is a difference between a movie like The Godfather vs. X-Men: The Last Stand. Which movie do I enjoy more? X-Men: The Last Stand. I would say that The Godfather is a better made movie.
It would be like comparing Linkin Park (a band I absolutely love) to a band like The Beatles (a band I absolutely hate), and trying to say that Linkin Park was a more talented band. Obviously, the more talented band is The Beatles, but I think the better music comes from Linkin Park.
Well, obviously The Godfather is a more technically speaking, better made movie, but IMO X-Men: The Last Stand is the better of the 2 movies.