To make special effects “work” you need a good director. One example- The special effects team in TF2 said that they had no idea how to block shots in a totaly digital world. Bay steps in, and the problem was solved.
As far as the whole TFROTF thing goes, Bay even said the movie was all about action. “Just give me action and i will fill in the rest.” Something that is rarely done well these days. Yes, the story plot was weak. Also, he was dealing with a writers strike while trying to complete the film. But the movie still made 1 billion world wide and counting.