To begin with, let me say that I actually enjoyed this movie a lot.  I was entertained the whole way through, I thought the effects were great, and I was still thinking about it a few days after seeing it.

But there were a lot of problems with it, as well.

1. It’s 2029, and we still have to send a live creature into space?  Come on, don't tell me we had to send a chimp into the weird space storm, and not just a probe.
2. When they’re on the station and “receiving all electronic transmissions ever sent on Earth” (uh huh) all sorts of familiar images flash by:  Hitler, putting up the flag at Iwo Jima, etc.  I’d think it’d be a little more likely to get random images of Murder, She Wrote or the Home Shopping Network.
3. When Marky Mark’s pod is caught in the storm, the little date readout is flipping numbers.  I suppose this is to signal to the audience “He’s traveling through time!!” but c’mon.  Unless you’re in a DeLorean with a flux capacitor, you can’t detect time.  So maybe Tim Burton’s just trying to say, the date readout’s wacked, he must be traveling in time...that's kind of insulting.
4. I was so disappointed that the humans spoke.  What set Marky Mart apart from all the other humans, except that he used Helena Bonham Carter as a hostage, and could open cages?  Why did Tim Burton choose to make the humans capable of speech?  To me this was this biggest change in his version, and I thought it took away a lot.  Maybe Tim Burton decided this was a better way to make a commentary on slavery and racism, but I preferred the humans dumb.
5. Okay, I loved the Heston cameo.  Especially the fact is was all about guns. 
6. What the hell was up with the ending?  It made no sense to me.  I can think of two possibilities:  it was either an alternate reality, or  the future.
1. Let’s say it’s an alternate reality.  I don’t like this, because there is absolutely no precedence for it.  Why should it be an alternate reality?  Time travel has been introduced to the film, but nothing about alternate realities.  It opens up the door to the idea that the rest of the movie is an alternate reality as well, which to me weakens the message.
2. Or, let’s say it’s the future.  This doesn’t make any sense either.  How is it that General Thade is now considered a hero?  Why is he considered to have “saved the planet”?  Maybe Tim Burton’s just opening things up to a sequel, and there will be a whole film about how, despite Marky Mark’s best efforts and blowing up lots of apes, humans are still slaves, and Thade is considered a hero.   Fine…but really now, doesn’t it seem a bit of a coincidence that the apes would build an exact replica of Lincoln, in the exact same place, when it’s thousands of years later?  Not to mention the police cars look the same?
7. By the way, I’ve been assuming the planet Marky Mark landed on was Earth, but of course, there is nothing that says so…it’s just a holdover from the first movie, and the first movie’s most powerful ending.  But there is no reason to believe it’s Earth this time, I guess.  When Marky Mark takes off, the planet doesn’t look like Earth from space—it has other moons orbiting it.  Hmmmm.
8. I read this in Slate: “Before Davidson leaves the ape planet, there's a quick shot of Limbo, the orangutan slave trader, rummaging through his spaceship and slyly pocketing something. Evidently whatever he pockets contains the secret to space travel. (Maybe it's a manual: "Space Travel So Easy, a Chimp Could Do It.") Thade, who's pointedly left alive at the end of the climactic battle, must have built a ship, flown into the time-warping electromagnetic storm, and landed on Earth at some point before Davidson returned.  Then he led Earth's apes in a rebellion against humans, took over  the Earth, and had the monument built for him.”  Okay, that’s a bit of a stretch, but sure.
9. I love the ape’s helmets.  During battle scenes, all I could think of was the Winged Monkeys in the Wizard of Oz.
10. Okay, why did the apes speak?  Sure, the chimps that crash-landed on the planet were genetically altered, but they couldn’t speak.  It would require quite a bit of surgery/evolution to develop vocal chords capable of human-like speech.  What would be the point?  Why would the apes bother to develop such a thing? 
11. There were orangutans, gorillas, chimps…they also referred to monkeys.  I thought only chimps were on board the ship.  How’d these other ones get there?
12. All the humans were white, with a few black and Asian actors.  I can imagine only a handful of humans survived from the space station crash…would we still see such differences in skin color?
13. Hmm, another theory I read:  they are on Earth, but they went way BACK in time, not in the future.  I like this theory. 
14. Okay, so you say, “Then what’s with the extra moons?” but if it was wwaaaaay in the past, I could buy one of the moons breaking up and disappearing.
15. Then again, I’ve also read Burton has said specifically that it was not Earth.  Well, he is dating Lisa Marie…
16. Okay, maybe there were only chimps on the space station, but gorillas and monkeys were already on the planet.  The chimps from the space station lifted the gorillas up to their level (or at least the level of being in the army.)
17. And why the heck was Marky Mark going to D.C., anyway?  Is that really where our future landing pads are going to be?  In 28 years?  Hmmm.

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