The original Planet of the Apes series was well steeped in time travel shenanigans, but it all pretty much worked out. At the end of the fifth film, the only complication was choosing whether the whole thing was one big loop or that the future had been changed for the better. Not too bad. The recent Rise of the Planet of the Apes skipped time line complication as well since the movie was clearly not trying to be in continuity with the original series.
Tim Burton's Planet of the Apes film was also separate from the original's continuity, but it has a tangled timeline just within itself thanks to its shocking twist ending in which bad chimpanzee General Thade somehow infiltrates Earth's timeline and changes everything into Ape-Ville long before Mark Wahlberg arrives back home. This alternate version of Earth apparently had its own ape Abraham Lincoln and everything (of course it was Thade, somehow). The logistics of this new timeline are simply too silly to contemplate without giving oneself a headache. For instance: if Earth had been run by apes since the Civil War, wouldn't Mark Wahlberg cease to exist?
