"Typical Michael Bay film"? What the hell does that mean? Show me a movie (let alone a summer action/sci-fi blockbuster) that's not loaded with cliche and melodrama and is also somewhat predictable, and I'll show you a movie that probably wasn't very popular among general audiences. You're going to have that stuff in a TRANSFORMERS movie, and in fact, the TV show and comic books even had it in spades, so get the heck over it.
I'm not a huge Transformers fan, but I love the concept, and I know the universe well enough to call myself a casual fan. This script, regardless of which draft it is, is not bad at all. Quite decent, in terms of structure, story and storytelling. Yes, it's loaded with cliches of every variety, but you know what? Every single episode I ever saw of TRANSFORMERS was a cliche. Ditto many of the comics. They were just cliches with GIANT ROBOTS. Which rock.
There are some fantastic scenes in PRIME DIRECTIVE. The character setup is fairly well done, even if there are a few too many of them to really matter. The stuff with the Autobots trying to hide is classic, as are most of the action sequences. The interaction of the Transformers with the government is handled well and fairly realistically, the relationship between Sam and Bumblebee is nice to see, and, perhaps most importantly, Optimus Prime is handled quite well. The Decepticons' roles could use some beefing up and some more dialogue, but they certainly seem malevolent and evil enough. One thing I really liked about the script was that the writers get that the idea of Transformers, giant robots who turn into cars to disguise themselves, is inherently incredibly cheesy, but can be damned cool at the same time. And they play with it, and the absurdity of it. I also like the use of metaphor, despite the lack of subtletly. "More than meets the eye" is a nice metaphor in the script, whether it feels like they beat you over the head with it or not.
The action scenes in particular sound massive, and fantastic, and if the CGI approaches anything good, we're in for a visual treat or two. Overall, the script seems to be about as faithful to the source material as any comic book movie/tv show script/project has been, and hits a number of very important points of the mythos well, so I'm not even sure why that's a complaint here. If subsequent drafts improved on this one's weak points, I'm looking forward to TRANSFORMERS even more.