This is just a more story/campaign based theory. It’s not about feautures or even every new aspect. More on the old, and some new.
The Story and Progression
I think the game will be slow and dark at first. The first few levels you are lone, fending off against some foes. You don’t know much, you and Cortana are exploring and slowly learning knowledge.
The game picks up and gets deeper and bigger. It will end up being the opposite of Halo:CE. In which the game starts off bigger and then drops at the end. In this I believe we will start off slow, alone, with no help. Yet ultimatly end up back in Human allied hands.
The Flood
The Flood will gain more access due to incompetence and curiosity. I think the remaining Covenant and even ONI will use the weaker Flood as a excuse to bring them closer to Earth planet(s). Then from there they will gain power and eventually regain a Gravemind
However due to recent theories it seems as if “The Timeless One” is linked to the Flood in someway. He may infact tie in this theory and be the one who ultimatly releases The Flood once more.
The Covenant
It’s hard to they are even a Covenant. From what I hear the Prophets left the Brutes and such, and the other species are pretty much useless without the Covenant.
However The remaining SPECIES of The Covenant are well beyond being done. Brutes and Jackals I can see becoming strong allies in the longrun and creating an effective “Guerilla” warefare style war against the UNSC, Even with there new tech.
Grunts I see becoming more excluded, Slaves to the Brutes in most cases. I see Grunts even switching sides and becoming “Good” and betraying The Brutes. The Unsung hero of Halo 4? Haha why not?
Elites
Elites I think will be the biggest story plot in Halo 4. Or at least a huge one. I hear from the newer books that ONI has been harassing The Elites and Arbiter. I would not be suprised if the Elites leave humanity alone. Yet once things get heavy you will be begging for help.
Yet since ONI was being -Yoinks!- to them I think the Elites will just ignore us. I think it would be a good story sup-plot if durring Halo 4-5-6 you had to regain the trust of The Arbiter and his Elites. Because of humanities need for power and revenge they will ultimately loose a great and powerful ally.
Back to The Covenant I think it would be a mindfuck of Elites and Brutes became allies in Halo 4, stronger then ever, using both of there stregths against Humanity. Elites hating Humans for backstabbing them and Brutes using there anger of humans in general.
And of course Brutes may start to like Elites because the Prophets are all gone and left them for death. Elites could possibly forgive the Brutes knowing The Humans are stronger and need to be put down. Before Humans become the evil of the Universe.
In other words
A Covenant with Elites and Brutes being strong allies and not being blinded by prophets and such. The other species may even join them. Making an effective enemy in Halo 4. However with no real FLEET the Covenant wont have it’s naval strength.
The end and such
1-Ending with a big battle. Almost a cliffhanger. Yet one like Halo:CE.
2-You may spend some time trying to get Elites back. Releasing you are “fuxed” without more help
3-Another Grunt Rebellion
4-Covenant coming back.
5-And on top of all this The Flood will come back for sure
6-Plus don’t forget the New Enemy as well.
So. Yea.