Keep in mind that this is not 100% confirmed officially. It is believable though, so I'll assume it is true for this thread.
Anyways, Ken Levine has said several times that they've made enough raw content for this game to fill four or five games with how much they have cut from the game over the five years of development. Considering that and the fact that they've spent nearly 5 years in full development, it's actually surprising that the pricetag for development wasn't much higher than $100 million.
Aside from so much content being thrown out or redone, the development of this game actually seems to have been pretty well-managed financially. The big issue seems to be that so much content was replaced or trashed, which is extremely costly.