Michael Bay has completely overreacted here and I don't blame Hugo Weaving for saying what he did in the slightest.
Here's the thing. Michael Bay has never attempted to make his TF movies even remotely deep compared to some of the lore that the likes of Simon Furman has produced. Countless people have defended it by saying you need to "switch off as a fan" to enjoy it. Bay himself has a reputation for only caring about explosions, car chases, half naked women and "making things look cool" when it comes to movies.
Now compare a role in that sort of movie to some of Hugo Weaving's work. You can't begin to compare his role in say "Oranges and Sunshine" to his role as Megatron. Certainly the character is iconic, but people need to ask themselves- is the role iconic in those movies (ie are we talking about a war-based character on par with say, the writings of Tolstoy)? If people are honest, they'd be forced to answer "no". Let's face it, spending 2 hours in a recording booth to record dialogue for a an entire part in a movie, is hardly going to be something you can sink your teeth in.
People criticise Weaving for only caring about roles he has alot of screen time in. However if you were an actor, then wouldn't the more meaningful roles be the well written ones you had the most chance to sink your teeth into, to immerse yourself into, to connect with the most.
Considering that, how can people be surprised that Hugo Weaving wouldn't rate playing Megatron that highly compared to some other roles? Furthermore if Michael Bay has a problem with that, then he needs to seriously rethink the types of movies he makes.
EDIT: It's interesting comparing the comments in this interview to the ones he made here
regarding his work on Oranges and Sunshine.