The actual intent of the ending (and why no one wants to accept it)

The intent of the ending (which is suggested by the film but not actually explained in any real way) is that Thade uses the Oberon or one of the damaged pods to travel back in time to change the Earth into a planet ruled by apes. The reason this ending isn't accepted by most people who watch the film and why they dream up their own convoluted endings is that it doesn't explain:
1. How earth apes where able to develop into species with an advanced intellect between the time Thade has landed and the time Leo does
2. How a single ape was able to overthrow the human population of earth with a single gun and only the help of modern day earth primates.
3. If the Thade was able bring back enough apes from his own planet to help him overthrow the human population of earth (or at least the united states) how he managed to do this and when exactly it happened in our earth timeline.

With so many gaps in the ending and no full satisfactory explanation there's a lot that is left for the viewer to piece together as to what exactly happened to allow Thade to rule an Earth dominated by apes. I don't believe the film-makers had in mind alternative universes or multiple parallel earths when they came up with the ending and there's certainly no hint of it in the film itself.

I guess the reason there are so many differing theories on the films ending is that when you have an ambiguous and unsatisfactorily explained ending in a film involving time travel people will come up with their own explanations instead to fill in the gaps in logic and commonsense that the writers weren't bothered with.