Final Wars definitely had signs of problems due to information leaks. The staff was blasting Kitamura because he was short changing the SFX staff to the point they had to make suits from older suits. We found out about the harsh language they had to overdub in NYC scene and the fact they made a black guy a pimp leaked out. The three composers they needed and the guy they hired to make a title sequence and all that money that was not properly spent on the movie was all known about before the movie came out. We all knew that movie was going to be a dud months before it's release. It probably helped that Norman England was friends of staff on the movie too. Granted he didn't personally leak information about the movie however I think some of his friends might have.

Who knows what is going on with this movie. It might have to do with Anno trying to make something work in live action that works in anime and maybe it didn't translate well so they caught it early. It doesn't sound like they are messing with their vision as much as they noticed something was really off. /speculation
With Final Wars, Toho pretty much let Kitamura do whatever he wanted minus the NYC scene where they forced change.