The problem with Bayformers (I'll just speak about the first one.) was that the Transformers, as in the guys in the title were taking the back seat on their own movie. We had the Sam Witwicky wants to score with Megan Fox plot. The Josh Duhammel and his wannabe Joes trying to return home. The Blonde and Anthony Anderson uncovering the evil conspiracy plot. After all those plots came the Cybertronians' quest for the cube.Also people complain that the Michael Bay's Transformers divert from established canon although Transformers has a large fan base its not big enough to make a film to make the kind of profits it made by making a movie which only appeals to hardcore fans. So any MOTU script has got to be good enough to entice a non hardcore fans and people who have never heard of MOTU.
What little time the Autobots had on screen, they spent almost half of it playing hide and seek at the Witwicky residence.
I am not saying that G1 was better... (They did some pretty stupid stuff back then.)