I've said it
before and I'll say it again. Of the five films under Bay's tenure, the first one is the one that most consider to be the most decent or most competently made. But when one takes a good hard look at it, it becomes clear that it really feels like at least two separate films mashed together.
On the one hand, you've got a military intrigue film about the U.S. Army facing an unknown enemy threat that has the Pentagon stumped enough to call in outside help from young analysts and hackers, while a small band of soldiers are on the run for their lives.
And on the other hand, you've got a whimsical coming-of-age film about a boy getting his first car in hopes of impressing the girl he has a crush on, and his car turns out to actually be an extraordinary being from outer space, who helps the boy get the girl and takes them both on a life-changing, whirlwind adventure.
...And somewhere in there, you've got a Transformers film with Autobots and Decepticons coming to Earth from Planet Cybertron and fighting each other over the AllSpark. This was used as the glue that helped tie those other two films together, but still really feels like Bay wanted to make the military intrigue film while Spielberg wanted him to make the coming-of-age film instead. Thus, the end result feels like a mashed-together compromise.
Consequently, because the film needed to hurriedly bring everyone together in its final act, some parts of this mashed-together compromise feel really underdeveloped. The aforementioned hacker subplot with Maggie and Glen gets hastily interrupted by having the two of them arrested and locked in an interrogation room for nearly the entirety of the film's second act, all to give more room to the other ongoing plot threads and to introduce yet another one whose inclusion felt really unfinished: Sector Seven. They just show up out of nowhere halfway through the movie to interrupt it for a while, only getting things back on track when they're suddenly used to bring all of the separate casts of characters together at Hoover Dam.
Sector Seven's inclusion might have felt more natural if there had been at least one scene earlier to foreshadow their arrival at the Witwicky home. Like, when Maggie and Glen are arrested, maybe show Simmons and Banacheck watching their arrest from afar, wearing their suits and sunglasses all mysterious-like. This would make us wonder about who the two of them are, so that when they both show up again later and formally introduce themselves to the Witwicky household and John Keller, respectively, the two of them and the secret organization they work for wouldn't have felt as randomly-inserted midway into the movie as they did.