Trevathan mentions to Mae that, out of all the texts and books he reads to him, Proximus is most interested in Roman history, and has primarily modelled himself and his ideal kingdom after the various figureheads from it. Proximus likely took a shine to this particular era when he found out one of the Romans' most famous and influential leaders was Julius Caesar (who of course, the apes' own Caesar was directly named after).
The final scene's implication that even by the time of this film no cure for the mutated Simian Flu has been found, and that those pockets of humanity that have retained their intelligence and technology are forced to remain confined to hermetically sealed environments to avoid contamination by the virus helps explain their inability to rebuild their civilization or reclaim the planet from the apes despite their technological superiority. They are literally trapped in their archologies, with only the handful of individuals like Mae and Trevathan being able to go on scouting missions, due to apparently being The Immune. Which also helps explain why reestablishing satellite communication would be such a big deal for these people: after centuries of isolation, it will finally allow them to start working together, at least as far as exchanging information goes.
The trailers for Caesar's trilogy always had a tendency to frame him and his actions throughout like he was an aggressor against humanity, leading the apes to eventual subjugation over them, either reluctantly or intentionally. The trailer for this film highlights Proximus' villainy — intentions for conquest, aggressions against peaceful ape tribes and hunting humans — whilst also framing the inquisitive Noa being confused, then horrified, then vocally objecting against Proximus whilst being intercut with scenes of him defending, protect and working alongside the "smarter than most" Nova/Mae. This is in fact the same type of manipulative editing, making us see Noa as a "good ape" for defending the helpless, defenceless and "innocent" Mae from Proximus' ambitions, whereas in the actual film, she is a lying, manipulative Unscrupulous Hero who lies constantly to the good-intentioned Noa to get him to help her in her mission, kick-starts the climactic confrontation with Proximus' forces in a manner that leads to the deaths of his soldiers and innocent slaves alike, and ends the film having set in motion events to potentially allow the remaining intelligent humanity to regroup and enact another destructive ape/human war, out of a belief that her kind "deserves" their old way of life back, even if it would come at a cost to Noa and his people. Just like Caesar is really The Hero of his films made out to be the villain because said films are made by humans and for humans, Mae is actually something of a Big Bad Friend to Noa in the end, but the film makes her out to be a Damsel in Distress that is reliant on his aid and goodwill to survive.
Mae reveals to Noa that she is seeking a book allowing "Humans to speak." Noa thinks this means that Mae means a paper book that will reveal knowledge of how to make non-verbal humans intelligent again. Mae really means an encryption disc that will allow for mass communication. Which of course is another way of giving humans the ability to communicate.
"Allowing Humans to speak", given the current devolution of those infected with Simian Flu, becomes another way of Mae saying that she intends to return humanity back to the era where they were the ones with the capacity to talk and apes were not their intelligent superiors, hinting at her underlying (and somewhat understandable) Fantastic Racism against Apekind, whom she has only even known as oppressors or scavengers of humanity's legacy who bastardise said works for their own benefit, like Proximus. Even bonding with Noa at best only seems to make Mae recognise him as "a good one" of his kind, and even then she still brings a loaded gun to their final meeting in case he turns violent against her, which Noa seems to sense and is further disappointed in her for.
Eagle Clan has complete disassociated itself from Caesar's legacy and the common history of apekind, which is reflected in the fact that they are shown to be developing a truly indigenous ape culture and society instead of one derived from human civilization. This is reflected even in their personal names, as unlike the coastal clan that still uses human names (Proximus, Sylva), Eagle Clan uses names not derived from human ones.
Noa's climactic confrontations with both Silva and Proximus have him (somewhat unintentionally) following Caesar's Ape Shall Not Kill Ape tenet (albeit in a technical sense), even if Noa does so because he knows better than to confront either one in their element of simplistic animal violence. With Silva, he's clearly outmatched and instead chooses to use his greater agility and the environment to lure him into a position where his bigger bulk works against him, leaving him to drown from the rising waters. With Proximus, he instead chooses to overcome his demonstration of his "right to rule" between them through violence, by instead appealing to the Eagle tribe's traditions that Proximus is ignorant of, his surrounding tribe members taking up the war call that Proximus believes is merely harmless chanting in support of Noa at first until the birds start bombarding him, attacking him in a manner that stops him from using his natural advantages and again takes advantage of their environment to push him to his demise.
This refusal to directly kill his own kind contrasts with Mae, who does deliberately and very vengefully kill Trevathan in a manner not unlike that of an unevolved animal, squeezing the life out of him with her bare hands. Her primary reason for doing so being outrage at Trevathan exposing "human" secrets for the Apes to monopolise hints at her underlying Fantastic Racism against apekind which, along with her brutal murder of her own species, marks her out as being less heroic than Noa, leading up to the ending reveal that she's actually something of a Big Bad Friend to him, believing humanity deserves to be the dominant species again even as her actions show her to be more savage and less "enlightened" than Noa — in fact, Noa's spiritual enlightenment is the entire reason he was able to overcome Proximus, and by the end of the film he too has wised up to Mae's manipulative character, even if he wishes they could still be allies. In contrast, Mae's experiences don't seem to have changed her outlook at all, and in fact seem to have reinforced them, with her at best coming to think of Noa as an outliner amongst his savage kin, and even that is conditional, as shown by her carrying a concealed gun to their last meeting, prepared for violence even if Noa himself seems disgusted that she'd think so lowly of him.
Noa's name is two-fold:
Firstly, it continues the biblical parallels from the previous trilogy. While Ceaser was compared to Moses, both helping to free their enslaved peoples and leading them to a promised land he could never enter, Noa is similar to Noah, helping to save his people from a great flood.
Secondly, Mae's first onscreen words being to shout "NOA!", calls back to Caeser's first word in the previous trilogy being a Big "NO!"
Noa giving Raka's 'Caesar' medallion to Mae at the end could also be interpreted as him subtly reminding Mae that the only reason she could get this far and even succeed at her mission at all is because she and the apes were working together. Without the help of apes like Noa and Raka and Noa's tribe, Mae's quest to return humanity to dominance would fail. For that, the medallion would serve as a reminder that even if Mae and her fellow humans succeeded in returning to dominance, it could only happen because they received help from the very apes that they hated so much in the first place.
Of course the thinking humans base is far out on the Great Plains, all the extant Great Apes are forest dwellers and largely stay that way after evolving, the only savannah ape around is humanity which makes the grasslands the last place the apes would want to go and a good place to hide a human base.
Also those "decayed" radio dishes are clearly nothing of the sort, the bunker inhabitants have biohazard suits and would be able to go outside for limited periods using them (just not being able to go very far) and could easily maintain the dishes but have made them "look" wreaked as (unlike the low lying base) they'd be visible from far away so anybody passing would simply shrug and assume more human wreckage rather than a working comm station.
Mae manipulates Noa by Obfuscating Stupidity, pretending to be a simple feral human so that he and Raka would treat her as a harmless pet and allow her to access the bunker. This is basically the same thing that Koba did to Carver in Dawn of the Planet of the Apes — he presented himself as a silly, stupid ape so Carver wouldn't realize how dangerous he was. This is a subtle example of Mirroring Factions that demonstrates both the usage of sneaky, underhanded tactics by both sides and the inherent danger of underestimating either species.
The presence of the Simian Flu throughout the prior trilogy led many to assume that Rise was the start of a new continuity and that by the time Taylor or the equivalent thereof managed to land on the future-Earth, it would resemble a much different planet than what he experienced in the original. However, with the satellites still being able to activate three hundred years after Caesar's death, and the bunker's contents being potential assets to Proximus, who's to say that the nukes might not be capable of detonating. Combine that with Mae's viciousness and desire to see humanity regain its status as the dominant species, we may be about to witness the nuclear war that left the Statue of Liberty destroyed. What was considered a reboot, may very well have been just setting the stage for the original after all...
