According to tweets by a staff member of game developer age, the director of Muv-Luv Alternative: Total Eclipse was changed from Inagaki Takayuki to Ando Masaomi (episode director of "Fairy Tail"). Apparently the production staff had put so many resources into the first two episodes and Inagaki had gotten overloaded with tasks. The staff said the studio has been in a mess which is probably noticeable from the quality of the third episode. Although the credits list the change in director starting from episode 3, Ando actually took over Inagaki's job starting from episode 10. Inagaki is now concentrating on making the scripts and the storyboards.

Source: Twitter account of age's staff