I wondered about the suicide note, too - it seems so mature for a 16-17 year old boy. That is why I've wondered about the age of John Doe , and if he might have been older than originally stated.
I wish we had some way of knowing the condition of John Doe's feet - he was shoeless and from what I've read, no shoes were found. Obviously if he had walked far, his feet would be scratched, cut, dirty.
The place where he hanged himself was not remote, but it was off the beaten path a little. If John Doe was not from the area, then the question arises as to how he got there and how he knew about the place. Perhaps he lived in the area in the past, or had relatives in the area.
The reason I rule out murder is that the suicide note is detailed regarding John Doe's feelings about not fitting in; his parents providing all the advantages; implications of past psychiatric care - how would the murderer know that the info he put in the suicide note would apply to his victim? John Doe might have been identified, at which time his family would read the suicide note and would have been able to tell if it sounded totally unlike anything John Doe had ever said or written before. And how would a murderer know John Doe wasn't an orphan, or estranged from his family - the note sounds like John Doe cared about his parents and wanted them not to feel blame.
I think if someone killed John Doe, it would be more likely he/she would have written a brief "good-bye cruel world" type of note.