Well, you did seem to have some good speculations, but they were thrown around with no order or connections between your ideas. I wouldn't quite call this an analysis of the plot, because it is just some factors that will come into play in the future.
Anyways, it does seem logical that ONI would be trying to greatly weaken the elites. The elites were the largest threat to humans in the human-covenant war and they served as military leaders for the covenant. They basically held the covenant together until they were later replaced by the brutes. ONI most likely doesn't want another religious war to occur from some radical elites trying to build up another army with goal of wiping out humanity.
ONI doesn't seem to trust the Sangheili, even if many of them do not want to fight the humans any more. They fear that another war will break out in the future and that elites will most likely be the cause of it. Now that humanity has the Infinity, Spartan IVs, and some new forerunner tech, they appear to be the more dominant race, because the elites have their own internal conflict. Humans will most likely go on a "power trip" and try to display the superiority that they gained. The actions of ONI in the future could play into the rumors that halo 5 will be the "darkest" halo yet
On another note, the precursors are most likely alive. Many of them were killed off in a ruthless rebellion by the forerunners, but others fled the galaxy to find safety. It is very likely that they have rebuilt their population in an alternate galaxy, and may choose to return at any point in time. I am not sure what their motives would be though, if they were to come back. Because they wanted humanity to inherit the Mantle from them, they may return to ensure that humanity has completed their obligations or something of that matter. Or, they may come to reclaim the Mantle that was once theirs
The precursors did also create the flood as a punishment for the forerunners. Not all of the halo rings have even been encountered yet, so the flood will likely be contained on all of those facilities. The flood was not completely defeated in the events of halo 3. This will probably be an important factor in making this the "darkest" halo game
and for the last part of your speculations, wasn't onyx destroyed?? I thought i remember reading that a team of spartans set of nuclear warheads in the core of the shield world