I'm not sure why this isn't being brought up, but I believe the man interrogating Dr. Halsey in the intro is the Master Chief. I'm thinking this is actually a scene after the events of Halo 4. He is back on Earth and takes off his armor...is going to see Halsey on his way?
And sure, Dr. Halsey knows what he looks like but he's kinda in the shadows and who knows how the Librarian's mutation affected John's appearance. The voice and tone is very much like John's.
http://www.youtube.com/watch?v=t1rYHczBMtE
Anyway, loved the campaign but I agree with the consensus that 343i should really flesh out the story
in the game and not have us rely on the outside material. Having terminals viewable on waypoint only was really a stupid decision, imo (unless there wasn't disc space?) I love the books; and really enjoyed Cryptum so having the terminals show us bits and pieces of the forerunner history was great. It's a lot more than what Bungie did with their lore in the game. So props for that. The potential to have an incredible campaign story within the game is there, and sometimes exposition dumps aren't a bad thing if it's the only way to present it; like the librarian scene with MC.