In the novel A Separate Peace, are there any frequent questions asked by the author?I've thought hard about it and have confused myself. I think...

A Separate Peace focuses on the relationship between Finny and Gene and the question of each of the boys individual identity.  The boys deal with insecurity, competition, friendship, jealousy, maturing, innocence, guilt, and war.

There is a co-dependent nature to their relationship, the boys depend on each other too much, especially Gene, who seems to be unable to make a decision without thinking how Finny will react.  His identity and his maturity is delayed because he is stuck in a cycle of needing Finny's approval.  Although this behavior is common among teenagers, who seek out peer approval and acceptance, Gene's personality is overshadowed by the stronger personality of Finny.

There is also the question of guilt that Gene has to deal with regarding Finny's injury and his eventual death. Gene's hidden feelings of jealousy erupt in a silent act of revenge when the boys are both on the tree limb waiting to jump.  Gene finally admits to himself and to Finny that he shook the limb ever so slightly which resulted in Finny losing his balance and falling, breaking his leg.

The two boys also have to deal with the war.  World War II, is part of their world, even though they successfully keep it in the background, believing that it will remain distant and not interfere with their lives.

The story also examines the effect of loss, particularly losses that Finny experiences as his accident and secondary injury change his life, removing his ability to play sports or go into the army.  Finny's character is seriously challenged by the leg injury, he is defiant in his denial of the limitations that it has placed on him.  Finny is somewhat reckless in his behavior, refusing to accept the disability that the injured leg demands he acknowledge.

Gene struggles with loss as well, the loss of innocence that he observes once Finny is permanently injured, and the world as they know it is changed forever.  Gene also must deal with the loss of his friendship with Finny and eventually the loss of his friend to death.