There are some things about Bay's directing of Transformers that I like, such as:
A: Portraying the Transformers as Giant Effing Robots.
This is something that has seldomly been so effectively done prior to the live action movie. G1 did a bit in the beginning, like in MTMTE when Optimus Prime kneels down and first talks to the Witwickies and other stuff like that. But Bay really gave us an awesome sense of scale - and one way he did this was through the use of a lot of low-angle shots... showing the Transformers from the human's POV - cos humans are like insects compared to the Transformers.
B: Nice and messy melee fight scenes.
I know some people don't like these, but I love them because that's what
real fights look like! None of that unrealistic rubbish from martial arts movies or professional wrestling etc. where it's all "clean" looking... when the TFs fight in Bay's movies it's one big messy brawl. If you've ever seen a real life fight (e.g. schoolyard, street fight) - just look at news videos of street brawls, they are
messy. Things fly everywhere and it's all blurry and all over the place. I personally can't stand watching martial arts movies - at most I'll watch them for the story, but whenever there's a fight I have to shut down the part of my brain that analyses movement - but I appreciated the realistic-feeling grittiness of the melee fights in Transformers and ROTF.
"I'll take you all on!" Raargh!

It also helps build that sense of scale too... as messy as watching people fight is, imagine how much messier it would look from an insect's POV where you're not big enough to see what's happening.
C: Bay's relationship with the U.S. Military allowed for some pretty cool scenes (a bit too much IMO, but still good). I think it's important to have the military involved because obviously if there's an "alien blood feud" happening on Earth, they'd have to do something. The military was involved in G1 (especially the comics) where the U.S. military established a special task forces exclusively for investigating and combatting Cybertronians (I.I.I., R.A.A.T.) -- and even S.H.I.E.L.D. was involved at one stage. I believe Transformers was the first movie that was allowed to film F22 Raptors. But the thing I don't like is how there sometimes seems to be more limelight and character development on some of the soldiers vs. the Transformers themselves. I thought N.E.S.T. was a pretty cool idea though (although the "America World Police" attitude was stupid... as
if the U.S. President could eject the Transformers from all of Earth. He could only eject them from U.S. soil, but if another country offered to harbour them there's nothing they could do -- the IDW comics showed this quite poignantly).
D: The relatively heavy use of real photography as opposed to lots of CGI.
Bay is like the opposite of George Lucas in the way that Lucas loves to use lots and lots and lots of CGI. He boasted that with Attack of the Clones and Revenge of the Sith, there was relatively very little that was shot on built sets and that most of those movies were shot on blue/green screens. Even the actors commented on how difficult that made their acting because they just had to imagine what the hell was happening. Bay on the other hand prefers to minimise his use of CGI and use as much real photography as possible. As a result it could be argued that his movies look more realistic and less animated. On the other hand, it could also be argued that Bay's methods are less environmentally friendly -- although apparently there's U.S. legislation now which dictates the amount of carbon emissions that movie makers put out. <shrug>
I think the TF movies could be better if Michael Bay just stuck to his job as director and just let the writers do their job. He's a great action director, but things get weird when he starts messing around with the script with things like, "Let's have him hump something," or "Let's make him pee on someone" etc. Yeah okay...