This is a tough question; I think the original Planet of the Apes series is best viewed as one epic story. However. In terms of overall quality, Escape From The Planet of the Apes is probably the best-- but I hesitate to vote for it because I can't forget that they expect us to believe that Cornelius and Zira roamed around the Forbidden Zone, somehow found the lake where Taylor's ship sank, somehow knew it was there, somehow raised it to the surface, somehow repaired it, somehow fueled it, somehow learned how to fly it, somehow launched it and somehow found their way back in time to roughly the same time that Taylor left. That's a lot to swallow.
That's just an example of what makes it hard for me to see the five films as one epic story. None of them, save the last, was designed with a sequel in mind. So each film had to retcon the rules of the previous film in order to justify its existence. In the original, there was no time warp; Taylor and his men were just in hibernation for thousands of years, maybe time-dilated by their velocity, but either way just in suspended animation. Beneath
had to retcon that into a time warp to justify a second ship coming to the same future. Then Escape
needed the rather absurd retcon you describe, and it introduced the revised backstory that the apes themselves were responsible for the destruction of human civilization after being bred into servants, rather than evolving in the wake of human nuclear war as the original indicated. (Taylor's famous rant before the Statue of Liberty only makes sense if he's directing his rage at humanity for its self-destruction; saying the apes were responsible undermines it, even if you say they were driven to it by human cruelty.) But Escape
implied that those events were a considerable distance in the future -- naturally, since it would've taken time to breed the apes into the more humanoid form we see. Yet Conquest
showed that the apes had somehow magically mutated into that form within a single generation after the previous film -- although at least they were almost all mute except for Caesar. But then Battle
retconned that and had all the apes able to speak. Ironically, Battle
was the only film that was written with the goal of allowing a sequel to exist, yet it didn't get one. (Unless you count the TV series, which retconned things even further.)
So while the idea was to create the illusion that these films followed on one another in an overall arc, they really don't fit together logically. Each one is a reinvention of the premise to some degree.