I doubt 343 would take that bigger move from the established game and mythos 2bh...
Thats not to say it doesnt have some merit, but does seem to go against everything the Chief was trained as since 6yrs old... theres still plenty that still can happen (uprising of the insurrection, the elite civil war from the kilo 5 trilogy, the possibility of the diadects return, not to mention whatever was happening in the E3 vid from this year) - without fast forwarding 20 yrs.
As for cortana, she was created from halseys flash cloned brain, and only 1 from the 10 worked - creating the first "cortana model" (she refrences that at the end of halo 4 which might be pointing to a new "cortana" somehow) now unless that is somehow linked to her being real (proper halsey clone anyone?) I doubt that is the case - shes likened to a young halsey in all the books as opposed a unique individual.
That said i do remember somewhere that cortana had a "sister" with a similar name, i forget where i read it from but i seem to remember she was like a Beta testing version,or Basic model, before they created the proper AI With all the code they wanted incorperated.
Like i said in another post, im sure 343 have something pretty impressive up there sleeve (new console, new benchmark) - and ill put 10 to a penny that nobody will guess whats coming before its released