I have read and taught "Paul's Case" many times.
It seems to me that one part of Paul's "case" is that he is gender-variant. There are NUMEROUS indications of this both in Paul's actions and in the wording Cather often uses when describing him. For instance, on the first page alone, she uses "hysterical" twice and "peculiarly offensive in a boy." Hysterical comes from the Greek "hyster," meaning womb. Could anything be MORE feminine?!
Paul does things which are more "typically" feminine than masculine-- looks at women only for their clothing, goes shopping the first thing upon his arrival in NYC, uses violet water (which he hides at home, indicating he knows it's not "right"), etc., etc. To miss these and as many more such details is inexplicable in any reader, in my opinion.
As in real life, though, Paul's case and ultimate suicide are determined not just by gender non-conformity but also by the rampant capitalism and fairly rigid class structure of his time, not to mention family issues. Paul also exhibits elements of narcissistic disorder and ADHD, both of which could make school frustrating in the extreme for him. But I cannot see how any of these other factors are as
prominent as is his being gender-variant (which is often but not always indicative of homosexuality, as recent studies have shown).
Paul may also be representative of the American who wants to "reinvent" himself -- and perhaps his life thus far has not prepared him to do it. But I still think the real hitch, even here, is that he acts -- due to his very nature -- outside the bounds of what society considers ok for males.
Remember, he seems to always be looking around him and to see if people are watching him and trying to notice something. What could be more typical of the feminine boy (or masculine girl) in a society where gender-variance is considered a reason for people to kill you?! The very way he moves his eyes is considered "peculiarly offensive in a boy"-- I don't think any valid reading of the work can ignore that.