Erm... this whole writup is pretty much a spoiler. You have been warned.
The unexpected (and nearly inexplicable) ending to Tim Burton's remake was in fact another "hat's off"... to the original book, rather then the first movie.
Of course, in the book it almost makes sense. In La Planète des Singes, the the planet the cosmonauts crash on is in fact not earth, but a world they call Soror (in the Betelgeuse system), which has unintelligent humans but apes with technology. Thanks to the wonders of relativity, less then two years had passed for the cosmonauts during their journey, while about 350 years passed for the rest of the galaxy. If I remember correctly, it turns out that sometime after our heroes had left earth, a faster form of travel had been discovered and the planet had been colonized hundreds of years before they arrived.
Like in both movies, apes had since taken over and humans had reverted to a more primitive nature (essentially out of laziness, in the book at least). Ulysse Merou (the Taylor or Davidson character) has to prove his intelligence (made more difficult because the apes don't speak French... why would they?), earning him the friendship of some apes, but instilling fear in others. He is eventually forced to flee back to earth (taking another 350 or so years) where he finds...
...apes have taken over his home planet as well (shock! shock! horror! horror!). The book also has a further surprise ending. From the beginning the reader has known that Ulysse's story is a "message in a bottle" found by Jinn and Phyllis, a wealthy couple traveling through space on vacation. At the end, they conclude that the story must be fiction, since it's unreasonable to think that humans might ever have been intelligent. Jinn and Phyllis are, of course, chimpanzees.
Pierre Boulle's book is actually pretty good, or at least the English translation (called Monkey Planet in Britain and Planet of the Apes in the U.S.) by Xan Fielding is. Not as theatrical as the first movie, and makes a different statement, but is better satire.
I don't claim to know what was up with Tim Burton's ending (or the rest of the movie, for that matter), but I suspect he was trying to capture the feel of the book as well as the feel of the previous movies.