Cain was able to create a special formula for the creation of skills...
He realized that relying solely on the system wasn't a very wise decision. That was because the system would never provide you with an answer to a question you didn't ask.
What this meant, was that while you might think you've got it all right because you asked the system, there would be many pieces of the puzzle you would miss because you either didn't ask the right questions or didn't ask enough of the right questions. All these factors could lead to incomplete information that could severely hinder growth.
Luckily for Cain, he was very observant, and he was able to notice all these things. If not, he would just roll with the information provided to him by the system without question.