When he landed on Earth it was 135 years after he had left it and in that time the Apes on Earth had taken it over. Don't think about it, there are huge holes in the story if you think.
Where did the Gorillas come from? Did they have them on the ship and we didn't see them? Why have large Gorillas when smaller apes could do the task? Horses. How the hell did horses get there? Why would they have HORSES on the ship?
The sexual tension between Marky Mark and Helena Bonham Carter was silly. Hey, T & A in movies is ok but the blonde didn't do anything but look good and act concerned, or jealous, about Marky Mark and HBC. Hey if she's just T & A we never saw her naked! "Loved" her sequined dress at the end though.
So the exterior of the ship deteriorates but all the wiring is intact, ready to come to life, after a few thousand years.
When the ape Prometheous (sp?) returns they should have played a distant Calvary charge horn, talk about a opportunity to return.
Just too much to go on. I was dissapointed.