The thing about the lead story writer leaving shortly before the release of the game he worked on since the days of Halo 2 was pretty suspicious back then already. Two most important members of the Bungie staff left (refering to Martin o'Donnell ... more like kicked in that case) the Studio quite unexplained and sudden. The community can only speculate on this (as far as I know). Surely that had a great impact on the development of the game.