After reading everything in this topic (and taking a couple vicodin for my headache) all I'm going leave with is
1. Cortana's not dead. She's trapped within the Domain.
2. The Flood should and almost certainly will make a comeback, possibly before the end of this season, though more likely it will only be alluded to and they become a new faction to fight in Season 2.
3.The Didact is dead, in a sense. It's possible he's still alive in the sense that the Librarian still lives through the Memory Fragment. And the use of the Didact's Memory fragment to influence various enemy motives would be understandable as well.
4. This doesn't really have anything to do with theorizing the storyline, but I would really like to see S-Ops start implementing new enemies. Want to see the return of Jiralhanae, Yanme'e, and maybe even start bringing in cut species like the Drinol and Sharquoi. Also New Promethean forces being awakened (maybe the results of the Composer being used on Covenant forces before it's destruction. I noticed the Covenant were nowhere to be seen after the Destruction of the Composer. Maybe he used it on them as well.)
Fear not, my brothers! The next generation of gaming is upon us! Be glad! A reward for all your toil and all your sacrifices is upon us.
There are those who said this day would never come. What have they to say now?
(Yes, I ripped off a quote from Halo 2 and modified it to my own purposes. Sue me.)