As far as Cortana goes, I mean they COULD revive her as a villain and instrument of the Didact but I wouldn't want that. Move on. Get a new AI with new quirks, with a different kind of relationship. I hate revivals or after-the-fact revelations that the player was deceived. They feel cheap and devalue what you already got.
That said, I still don't know how to feel about the Chief/Cortana relationship. I honestly didn't feel any emotion or empathy for the Chief. His last line being delivered without even a slight change in tone from his usual speech ruined it all. Plus it was a corny line.
And then there's how this ties into the man/machine theme. I mean I can see the link but I don't feel it. It's like they want to develop Chief into a character that is cognizant of this duality, but his "man of few words" nature is still getting in the way of this, even if Halo 4 probably has the most Chief dialogue of any Halo game. And body language isn't enough either, though I did think the most humanistic thing I've seen Chief do was rapidly spin his head at The Librarian when she told him that he (humans) was the greatest enemy the Forerunner have ever faced.
I think now that they've got the eyes out there, I absolutely wouldn't mind just seeing Chief's face in the next game throughout. They want to make it more personal right? This is the next logical step, and this is the perfect opportunity. Showing even his eyes was a huge step and it seems like nobody is up in arms and this isn't taboo anymore, so they should just push it all the way.
I can't imagine playing as insane Chief though, it'd be too weird for someone who has been the embodiment of pure good in the series for a decade. I think that kind of stuff would have to be purely restricted to cutscenes, which obviously contributes to creating some dissonance between the gameplay and story, which is usually a bad idea. We already had Chief defy orders for the first time in Halo 4, and maybe it's instead time for him to play a more political role in the UNSC and question the war machine at large with the unique perspective he has to offer. Especially after everyone except Lasky is treating him like any other soldier and not the bad motherfucker who just saved your galaxy for the umpteenth time.
And then there's all the possibilities regarding his Forerunner augmentations... So many variables with regards to Halo 5. And I like that. As much as everyone else it seems is being a Debbie downer on Halo 4, the story and game at large shows promise. Keeping in mind 343 is a new developer, this is likely them just trying to catch their bearings. To be a new dev and to still put out something like Halo 4 is commendable IMO.