What is the message in Frankenstein that Mary Shelley presents to those who would play God and ignore humankind’s natural limits?
The short answer to the question is that the message presented is that "bad things happen." Shelley's genius is presenting the idea that human beings are capable of accomplishing extraordinary feats. However, there are natural limitations and in ignoring them, bad things tend to happen. Victor exceeded these parameters in creating life. Sure enough, when he realized the folly of his action, it was too late. When he failed to understand the emotional implications in creating life, it was too late. When he could no longer control his own creation, it was too late. The adherence to either a natural condition where humans are content with their limitations or seeking to overcome them with the full understanding that there is a line not to be crossed, a frontier that lies in the distance not to be interrupted, becomes one of the driving forces in Shelley's work in seeing the predicament thrust upon Victor and the Monster.
The basic message that she is sending out is that when you dwell on situations that are outside of your immediate control, you are bound to lose control of yourself. In other words, Victor tried to meddle with elements that are commonly outside our reach: The first law of physics clearly says that matter cannot be created nor destroyed. He tried to create something regardless. Here , two things could happen: Either he could do something coming close enough to "creation", or something supernatural that he will never be able to control will come into play. The latter is what happened. He played with fire and got burned. He tried to stretch his God complex as a doctor to make it a reality and he ended up being the victim of himself.
Therefore, the lesson is: There is a reason for limitations. If there were no limitations our entire lives would end faster than they begin. That is what happened to his.