1. Ceasers son was a chump, he didn't do much and for all that you didn't really get a sense of who he was. he was just kind of there for most of the movie until the plot called for him to do something...semi heroic.
2. The reasons the humans were even in conflict with the Apes was ridiculous. The whole reason the war started was because people needed power, even to the point one of the characters says "They don't need power, electricity, thats what makes them strong" Humans have been around for around 5k years, electricity has been around for about one hundred and fifty...it's pretty clear in that type of scenario, going to war with the Apes at that time would have been foolish, Humans could have blew up the bridge, built alternative sources of power, then attacked the Apes by ship/all those damn skud missiles they had when need be, finding out exactly where they are. Apes can't swim that good and they were on an island...isolated, ya could have taken your time to dispose of them properly instead of rushing for power...power you don't really need.
3. The "good guy" human was so wack. He wasn't very smart and wasn't a very good character. Plus his son was shallow, "He's seen things no child should have to see" but still is to soft to really make a difference when the Apes attack.
4. The villian human(Gary Olderman) was wack also. His little plan to blow up the building didn't work...like at all, it' just made Ceasers fight slightly more interesting. He didn't even have that much to do in the story, he was very shallow.
5. Lastly, there were a lot of pot holes, once glaring one, Olderman said "We have contacted someone else" but in the scene right before that he is talking about how he they haven't made contact with anyone...overall the script wasn't very well written.