Oh, I dont think they were intelligent.

They just wanted to escape

Yes, he was just freeing them from captivity. As for the question about whether or not the ones from the lab were smart, I know for sure Scarface was (Not sure of his name). However I do believe the others from Gen-Sys were as well since I am sure Jacobs proceeded to increase testing, which is what caused Franco's character to quite his job.

I am almost positive that the monkey on the testing table during that scene was not Scarface.

That would make sense since we see on the TV screen (When Dodge bitches about his cookies) that the first expedition to Mars has begun and later you see in the paper "Lost in Space", which is most likely in reference to that expedition. It would tie in perfectly with the originals.

Other than that you have the contagious virus caused from ALZ-113. The ending points us in the sequel going in this direction.

We already know what happens hundreds if not thousands of years in the future with this franchise. I would rather them keep the focus on what ultimately leads to the Earth becoming dominated by the Apes rather than just another trip to an Ape run planet.

Yeah, there is basically two direct sequels they could do.

They could skip past the intial push of the virus accross killing all humans in a matter of a few months (movie showed it only took about a week to become deadly) and then focus on the new super intelligent apes (as they came into contact with dying humans they contracted it and became smart) that are now becoming the dominant species. This movie could follow a war of genocide as the very small % of humans immune to the virus stage a final stand and of course eventually die off.

They could  also simply redo the original movie where that lost mars exploration returns well into the future and well, you know the basics of the rest.

I personally want to see the first option as it seems far more interesting, then they could show the third movie, however, it will lose part of its appeal as the audience will already know which planet they are actually on.

Good point man that's exactly what I think too! My friend I saw it with didn't notice that thing about Mars and he doesn't believe me that it was there. It makes perfect sense like you say. 

My reasoning for the apes from the zoo becoming intelligent are apes are known for imitating. So since the apes that were freed from the zoos kinda imitated the smarter apes.

The humans die of a disease then the apes take over. The apes never fight the entire human race.

MASSIVE SPOILER!!!!!!!!!!!!!!!!!!!

You must of actually paid attention. (select all the text in the black area to read)

While they surely woudl have went hunting, the redwoods would have provided a lot of room for these highly intelligent apes to stand their ground, hide, evade, etc. Then within a month as the massive virus would have been infecting the entire world... they would not have been a concern anymore. Additionally, as the virus spread to areas with more apes... they would be contracting it too and becoming intelligent as well as beginning their own reprisals against the falling human race.

Its this combination of the dual affect of the virus and the timing of it all that causes the eventual outcome. It really does fit together nicely.