Ninja vs. Dr. Zaius who wins in a fight?

ninja had no such thing.

Stop nuthugging a fraudulent martial arts style.

There are no ninja and anyone claiming to teach ninjitsu today is either an outright fraud or they teach other styles under the name of ninjitsu, which they use solely for marketing purposes- still an unscrupulous act.

so basically what you are asking is would a person who was duped into learning a style of martial arts that doesn't exist anymore (and there is debate as to whether it ever did historically) be able to outsmart a genetically altered chimp that was the smartest chimp in planet of the apes.

While Dr. zaius was not the intellectual equivalent of a modern physician (in the real version of planet of the apes thier society and medicine was not very advanced, maybe to the level of the 1700's if that) I find it hard to believe that he wouldn't be able to outsmart a gullible modern day human. While his knowledge itself might not equal modern science, his wits are clearly superior to anyone that would fall for the "ninjitsu" sham.

He is also more physically superior to even a well-trained human as he would have several times the stregth of one. But here we are not even talking about that- we are talking about somoene who is the product of a Mcdojo.

This fight would go to Dr. zaius hands down.

The ninja must master the mind as well as the body grasshopper. The Ninja kicks Dr. Zaius' brains out!

the pirate would step in and plunder every body's booty muhahahahahhahaha