misguided at Bay.

Yes, Bay deserves some blame because the Transformers were nearly impossible to tell apart once they were battling and Skids and Mudflap were horrified but the main problem with the franchise is that Spielberg said it should be about a boy and his car. NO! It's about big fucking giant robots fighting over the fate of the Earth (and, to a certain extent, their own race.)
Too much of the franchise wasted time with Sam Witwicky, who would ultimately become pretty fucking useless in the climatic scenes of each film since he's a little dude and it's a battle of monstrous robots. It's like if the Avengers spent less time on The Avengers and quintupled the time spent on Hawkeye and Black Widow's relationship problems.
On top of the focus being too much on Shia and Megan, it also meant that there was nearly nothing more than archetypal characters and personalities for the Transformers, you know, the guys the franchise is named after and the reason people are going to the movie.

Add into the fact that Whedon is better with dialogue than Orci/Kurtzman could ever dream to be and the Avengers wisely used previous movies to establish the characters and you get a more entertaining film albeit still cliched and, more often than not, illogical.