One possible thesis statement for The Perks Of Being A Wallflower could compare and contrast certain elements of the novel or style of writing with another similar novel. For example you could compare and contrast the themes in The Perks Of Being A Wallflower with the themes presented in the novel Catcher in the Rye by J.D. Salinger. After all, the two novels have much in common. The Perks of Being a Wallflower is a tale presented as a series of letters written over the period of a year to an unknown recipient addressed as "Dear Friend."
We guess that this "friend" is a person Charlie has never met but who may be his senior. He wants to be able to trust this person, guessing that this is possible after he found out that the friend had the opportunity to take advantage of a party guest but chose not to do it. In Charlie's opinion this constitutes grounds for the "friend" being a "good" person. Here we have a possible thesis argument, as loneliness or isolation represent a key theme in each novel.
Another theme could be education (or school). It would be interesting to compare and contrast the attitudes of each student with their educational setting and this may lead to a consideration of the theme of "change" or "context" especially where this impacts the young person socially in terms of social resilience and emotional well being. Other themes could include failure, success, personality challenges, hope and disappointment, the meaning of life, reality and fake life, student observations, closure and mental health.
Holden Caulfield often seems isolated and this is worth exploring in terms of his own choices. Mental health issues such as depression and suicide are relevant too, as in a way, both students seem to choose to communicate with readers they don't know rather than to seek help from professionals or peers. Holden's attempts to connect lead to mixed results and some are very negative. His perception is that he is often taken advantage of which is quite serious as some of the people he visits are adults. He seems to trust those younger than himself a bit more, but then he feels a scary responsibility towards them. This, and other challenges, lead him into escapism and towards putting himself at risk. However he chooses not to take advantage of people either, but we are left unclear as to the motive for this. Readers may find it fascinating to discuss whether this makes him a "good" person of itself. Are there other reasons for his unwillingness to take his opportunities where he sees vulnerability? Or is it a sign of hope and belief in the young?