Too many chefs in the kitchen and changing game play requiring story changes? Throughout it all you can tell what they're going for, but I think it is the small things that inevitably have larger repercussions. Spartan Ops was almost irrelevant for the story, Halsey amputation and revenge, Jul M'Dama and Janus Key. For example, look at the MCC advertising. "The seeds of our future are sown in his past". Locke and Arbiter discussing Chief in H2A cutscenes. The Halo 5 reveal trailer shows Chief rogue with a broken helmet with Cortana chip and he finds what we thought was a Sphinx now Guardian. I bet once Tim Longo brought on, and gameplay becomes a squad shooter ala Republic Commando, story changes to incorporate more than just Locke hunting Chief, they then need Blue Team to complement Osiris team etc.
The E3 Halo 5 gameolay video had a far more dynamic Chief hunt and Hunt the Truth advertising promised an almost one step aheas Chief, find clues as to why Chief did what he did etc. So by H5 launch, the story is vastly different than what they wanted.