What if it turned out in the film that it wasn't even Ripley at all, but the Hive superconsciousness infiltrating the mind of the new protagonist, and everything Ripley says to her turns out to lead her further down the path toward the protagonist becoming the antagonist, and becoming hijacked by the Hivemind by the films conclusion, after slowly and painfully being absorbed at the genetic level into the Viral Overlord of the Aliens (the self-aware biotechnology that rebelled against and enslaved the Engineers driving them to extinction). What if Newt never existed, and was a figment of Ripley's latent instability result from losing her daughter (Amanda Ripley) and outliving her by decades? What if the Hive (through the Acheron Queen) was manipulating Ripley the entire time to try to assimilate her?
You could take the motherhood themes from Aliens and warp them and spin them and twist them into something truly horrific and abominable. The plot could involve mind control through dreams, and the alien energy that streams into the mind of an unconscious host of the facehugger/chestburster, and the connection of the Hivemother/Ultramorph with the other Aliens and those that had been chosen as hosts during any given infestation, yet managed to escape. The idea of an Alien of All Aliens warping peoples' minds and driving them into submission from lightyears away has always seemed fittingly Lovecraftian and snugly at place in the Alien series, and the idea would be that this Ultramorph and the Xenomorphs are mere appendages of a metaphysical primordial entity that has lain dormant beyond the laws of time and space, manifesting itself via rampant self-aware biotechnology that had literally evolved to become a 'second nature' (that Giger theorized about in his visions) and a rogue pocket dimension unto itself slowly tearing apart the fabric of spacetime through the effect of the observer (host) on particles and quantum physics. The Engineers did not invent this technology, and they were not the first to stumble upon it. It is the immovable, unstoppable, eternal counterbalance to natural organic life, the physical embodiment of raw nature and an Alien God.
In this way, the Alien Hive would function as a nation-state unto itself. Armed Forces (Xenomorphs), a Head-of-State/C-in-C (Queen/Ultramorph), language (telepathy), and a culture revolving around their eternal and unconscious service toward the spreading of... not democracy... but the genetic code that will unite all life throughout time and space with the True Messiah and the One True Mind. This could be further highlighted by having human government structures (i.e. a President) to contrast it with, and it all circles around back to the original political themes of Alien and Aliens (the Company, Special Order 937, etc), having it culminate in one final battle between warring Genetic Nations. Not a battle of firepower though, but primarily a Cold War, fought through the fragility of sanity and the omnipotence of fear. Fear of the unknown. Fear of the strange. Not Man v. Nature. But Nature Unleashed. Nature Unchallenged. Perfection Through Chaos.