So here's where we get to play "What Should've Happened?" During the Visual Effects Society Production Summit over the weekend, 20th Century Fox post-production president Ted Gagliano revealed that, originally, James Franco's character died at the end of Rise of the Planet of the Apes during a final showdown in the woods. But only a month before release, they decided not to kill him off, and brought both Andy Serkis and Franco back into the studio for reshoots, leaving us with the somewhat happier ending you all saw in theaters.
There was no reason given for why they all of a sudden changed the ending, though it may have had to do with both audience testing and the fact that early buzz could lead to more sequels, which meant they'd want to hold on to their lead human star so the audience could continue following him on his journey. But that doesn't mean Fox is completely finished with their original ending. Gagliano later added [via THR], "The other thing we really want to institutionalize at Fox for these after markets, is the importance of alternative scenes and supplemental material. For example, we thought James Franco's character should die (in Apes), so we are going to sell (the alternative clip) down the road.”
You'll get to decide for yourself what the better ending should've been when you can watch both versions on Blu-ray or DVD down the line (which is always confusing, storywise, but those alternative endings definitely help sell product). In the meantime, let us know which ending you think makes the most sense.
For more, check out a page from the original script below (courtesy of The Playlist) which shows how Franco's death was written.