>>714342921
I think in this case it was because The Initiative was set up to be Xbox's Naughty Dog equivalent that would win every GOTY award and unanimous critical praise, so it's likely:
1) They were trying to be perfectionist in too many areas even if it didn't have a big impact on the gameplay.
2) They wanted to have a hard-hitting prestige narrative and the issue with narrative focused games is you have to throw out and redo a lot of work if you change the story.
I imagine this game ran into similar problems as Ken Levine's project.