I've come up with a radical new idea (hence the title) for the explanation of the ending.
Apes and humans live in peace after Marky leaves. Daena and Attar lead the co-operation efforts. Unfortunately, mankind is smarter than apes and once they regain their place in society, they start to redevelop guns, nuclear technology - evil in other words. Since man is evil (yawn). They then start to think: If we're smarter and have better technology, why not rule this planet? They start a war against the apes and start wiping them out. Some apes desperately take refuge, steal some human technology (lasers, nuclear technology, space travel, etc.) and fly away from the planet.
The planet they leave becomes a planet ruled by humans again.
When they get to Earth, they find their technology is now superior to 1900 humankind, and still furious with humans on their planet for wiping them out, they go on a revenge kill-and-destroy mission on Earth. This is what Marky arrives back to.
So Earth becomes a Planet of the Apes, while the original Planet of the Apes becomes a planet of humans again.
Now, before everyone starts replying, bear in mind:
This is not my serious explanation - my real theory is a previous post which has been discussed aplenty. It's just a highly conjectural, creative idea I came up with and thought I'd share because I think it's quite funny for the planets to basically switch roles. I also don't think it contradicts any known facts in the movie. Let me know if it does.
