He can do a decent job when he is under control by someone higher than he is. When he is given full reign, things go haywire. With the box office success of the previous film, I doubt that he has been given anything less than full reign.
Keep in mind that the issues we have seen with ROTF and even the first film, are not isolated to Transformers but can be observed in his other movies too. Bay already had a reputation before he took the Transformers film franchise and although it has since been amplified, it hasn't really changed.