Reading Burton on Burton, a collection of interviews Tim Burton has done through the years, it would seem Tim Burton doesn't really know either, except he didn't want to copy the Statue of Liberty ending:
"We just went back to the overall mythology of Planet of the Apes, of the book, even the other movies. For me the whole thing has got a sort of circular structure to it, it goes round on itself somehow - parallel universes, time travel, man/ape, evolution, religion. Where do we come from? Where are we going? Do we just keep re-evolving? There was a feeling of wanting to do something where it was a parallel world but it was all apes, and there was something about that I liked - I had this image of a weird twisted parallel universe. I thought about it in a big picture - even though I couldn't give a shit about sequels, but if you do something like this you think about a bigger picture of the material. So there was the idea of going back in a sort of twisting of time, and again going through this juxtaposition of human/animal, and coming back into a world where you think its normal, but something has happened."Or you could just paraphrase it as: "Hey, I had to end the damn thing somehow..."
Geek film note: Nightmare Before Christmas afficionados might be interested to know the scarecrow designed to keep everyone away from the Ape holy site (which is actually the crashed spaceship Oberon) is modelled on the King of Halloweentown, Jack Skellington.