Koba is a bonobo, an ape soecies that is known for being peaceful and sociable unlike their more violent and warlike cousin the chimp: which Caesar is. Both Caesar and Koba have defied the very nature of their respective species due to their differing upbringings and their intelligence granting them morality: Caesar was raised by loving humans and thus chose peace and compassion, while Koba was raised by abusive humans and thus chose hatred and violence.
Koba tells Blue Eyes that his scars make him strong. Koba received his from abusive humans, which resulted in his intense hatred for them. This is a clever foreshadowing of Koba's (initial) influence on Blue Eyes's opinion of humans.
Given how it's pointed out from the beginning that human civilization crumbled in the 10 years leading up to the film, it might seem like a coincidence that Dreyfus managed to contact a military base for reinforcements rather than, say, another survivor group. That is until one realizes that the C.D.C. in real life (and the U.S. Government in general) is known for anticipating potential dangers to the point of being Crazy-Prepared, including a zombie apocalypse. Coupled with Dreyfus having a military background, it wouldn't be surprising if there were at least a couple of safe zones and military facilities still functional out there.
As well as the fact that, in such an event, many survivors would be likely to flock to a military base; It's a sturdy shelter, with weapons, supplies, and (most likely) authority figures. The military might even be recruiting survivors to keep numbers up.
Doubles as Fridge Heartwarming: Why was Caesar's second son with his father and brother, instead of his mother? Because, as we discover later, Cornelia was very sick. Caesar wanted to let his wife rest a bit and decided watch to over their baby son.
Also, baby chimps are not as dependent on their mothers as humans are; they're born with significantly better motor skills than we are, and develop significantly faster.
Everybody was surprised when they saw that the apes could talk. Most of the audience must have thought: they should have known, it happened in the previous film. But... should they? Apes did not talk during the big fight in the bridge, and only one person heard Caesar's words in the woods. There's Caesar's Big "NO!", which is recorded, but it may not be enough to start a big social or scientific commotion just yet. People could have thought that it could have been a noise that sounded like a "No", a sound learned by imitation... or, more simply, just a scam video. Who would have taken seriously a video with an ape talking? Plus, the Simian Flu must have been distracting everybody away from such mundane concerns.
Caesar declaring Koba to not be an Ape wasn't a No True Scotsman argument, at least not entirely. Koba cited that Ape shall not kill Ape; but following that logic, Koba (having murdered Ash and knowingly attempted to kill Caesar) no longer counted as an Ape. Granted, he was entirely willing to overlook that contradiction, but it meant all Caesar was doing was holding Koba to his own words.
Koba's last words are another Fridge Brilliance. Caesar's main teaching is that Ape Shall Never Kill Ape, which Koba considers to be weak. If Caesar helps Koba up, Koba will simply kill him. If he lets Koba drop, he will violate all of his teachings. Either way, Koba wins. If he lives, he can just take leadership of the apes again. If he dies, it will mean Caesar will have to live with the fact he violated his main commandment.
Which might make even more sense when he has an Oh, Crap! face. Caesar found a hole in Koba's logic and poked it so hard that the code wouldn't apply to him.
Ash's death was actually foreshadowed. First, he was in shot close ranged by Carver. Then, he was brutally murdered by Koba. Both Carver and Koba are human and ape counterparts to each other.
Koba's Last Word (a Big "NO!") make him an even more perfect Foil to Caesar than previously thought. Caesar's first spoken word is also "No", which he spoke to courageously defy Dodge Landon of the first film and launch the apes' breakout from the sanctuary. Koba screamed out his last word of "No" as a selfish, cowardly reaction to his realization that he was going to die. Before that, he had never once used "No" to demonstrate his courage and his compassion for the other apes.
When watching the film alone, Koba pulling off a convincing performance as a dumb ape when interacting with the two guards at the armory may seem a little silly and somewhat out-of-character. After reading tie-in materials that explained Koba was a Television star in his youth before becoming a lab ape, it makes perfect sense.
It's also worth noting that Koba starts doing the trick after one of the guards calls him a "son of a bitch." Only one other human has ever called Koba that; Tommy, the man who taught him those tricks.
Though it's a little vague because of his animalistic voice, Koba pronounces English words in British. At first, that may seem to come out of nowhere in the story itself (a simpler, behind-the-scenes explanation would be the fact that Koba's actor is British), but think back to Rise. Steven Jacobs, the head of the laboratory that had abused Koba for so long, and the one human Koba had it out for the most, has a British accent. With that in mind, it becomes a very fitting trait for Koba, considering how he progressively becomes humanlike despite hating them with a passion for the duration of this film.
Why is Caesar such a good fighter despite never fighting other apes before? He grows up in a much more nurturing environment compared to his peers. Apes like Koba have been mistreated by humans their entire life, so their physical development is probably a bit more stunted than Caesar as a result. Caesar also has the advantage of being exposed to human media, so he is a lot more Genre Savvy when it comes to a fight.
Another reason why Koba loses the fight against a wounded Caesar: His body is not built for combat. Bonobos are known to resolve their conflict peacefully, unlike Chimpanzees who are very capable of violence. Even though he is sentient and very vicious, Koba still has the body of a Bonobo, which is much less suited for a fight than a chimpanzee like Caesar.
Just how many innocent people did Koba and his followers kill?
How much pain was Caesar in after getting shot by Koba? That being said, what kind of pain did he go through when Ellie was fixing him since there was no morphine.
Since the Simian Flu broke out millions to billions of humans have died. That being coupled with Will and Caroline's absence... They're most likely dead.
Rocket has now lost his (presumably) only child by the murderous hands of one of the apes he called family.
Even if the peace between humans and apes remained intact, a couple of years later the settlement inhabitants would have caught a special strain of Simian Flu and become mute. Even worse, considering the Colonel's attitude towards the apes and their human supporters, making contact with him would bring a lot of problems to the Colony even without Koba starting the conflict.
