This probably belongs in IMHO, but, what the heck.
Here’s my take on it. First, everyone speaking English is explained by the fact that the apes and humans are all descended from the survivors of the mother ship, all of whom spoke English.
The ending is more problematical. What we know is that Leo goes through the time storm and arrives on the POTA. We assume that he goes forward in time because we glimpse his time indicator going forward. The Oberon follows him, goes throught the time storm, and arrives on the same planet, but thousands of years before Leo gets there. We hear a snippet of a log that refers to the planet as “uncharted and uninhabited”, at least by intelligent life. One of the apes, Seamus, leads a revolt against the humans and thousands of years later, we have a society dominated by apes due to their superior strength.
Leo arrives in this time, organizes the human revolt, and leaves when General Thade is locked up (but still alive, and very angry) and it seems that humans and apes are prepared to develop a society where they respect each other. Then we have the ending, where he arrives back home in his own time, on a planet gone ape, and on which General Thade is a celebrated historical hero who finally helped the apes gain dominance over humans.
My interpretation was that Leo and the Oberon actually arrive on Earth thousands of years in the past, before humans were the dominant creatures, or perhaps just before the advent of human civilization 6000 years ago. This explains the presense of the horses. The Thade memorial shows us that, with the absense of their savior from the stars, the peace was short lived, General Thade was released alive, and managed to lead the greatly outnumbered apes (who are outnumbered by humans 4-1) to a military and technological revolution. Thus, by leaving, Leo ensured the dominance of the apes, which may not have happened otherwise.
Don’t get me wrong, I don’t think this explains all of the holes. How likely is it that the Thade memorial would be exactly like the Lincoln memorial, and similarly located at the end of a reflecting pool? The black and white police cars, the Washington memorial look-a-like, etc., don’t make logical sense, they are obviously meant to fool the viewer into thinking this is our Washington, D. C.
There are other plot holes: why are there so many species of apes? I counted baboons, chimps, and gorillas. They should all have been chimps, having been descended from the survivors of the Oberon. Why are there only three species on this planet (humans, apes, horses)?
But given that this is Tim Burton, the story actually makes more logical sense than usual.
I kinda liked it, but I won’t be back for a second viewing in the theater or on video.