According to this GameRush report, Bungie really was fully prepped to go ahead with its Halo reveal at E3, with a a gut-punch trailer waiting in the wings.
“Bungie had a 60-second, knock ’em down teaser trailer made that was going to unveil the game and it was going to be the close to Microsoft media keynote at E3,” Jacob Metcalf explained. “This was going to be followed up by Bungie doing their separate press event later on in the week on Wednesday to show off the new game.”
“Microsoft has never really explained why they prevented Bungie from going on with their media event on Wednesday at E3. It has to be a new Halo game since if it was an new IP Microsoft would not have their hands on the control of the brand and would not have had the power to silence Bungie about it.”
If the Microsoft press conference had finished in a Halo reveal followed by the FFXIII announcement, the internet would have actually melted. C'est la vie.