(the big city battle lost a lot of impact for me from being so similar to the one in Dark of the Moon)
Well, I haven't seen that Transformers
movie, but there were a couple of features about the Avengers
Manhattan battle that stood out for me and that I doubt would've been true of a Michael Bay action sequence:
1) The focus stayed on the characters. Although there was plenty of destruction porn, the characters of the Avengers and their particular traits remained at the forefront of our attention: Captain America inspired and led people, Widow was fearless and resourceful, Hulk was mainly in it for the smashing but came through for his teammates when it counted, etc. The most important beats weren't explosions and crashes, but character moments.
2) The civilians weren't ignored. The heroes' first priority, as it should be for superheroes, was to protect the innocent and rescue the endangered. Even in the middle of this huge apocalyptic battle, they were taking the time to free people trapped in buses and coordinate evacuations and rescue hostages and so on.