I'm terribly sorry if I'm repeating something already said in this particular thread - I'm having trouble getting some pages to load - but surely a lot of Jon's issues come from his status as a bastard which is societally imposed rather than particular to Cat's treatment of him.
Jon has trouble with questions of entitlement - he's been brought up with no certainties about what his place in life should be. He feels keenly his difference from his siblings. He yearns to be more completely a part of the family, but he is set against the idea of a family of his own because of his own status. He has all the ambitions of a high-born lord, and the guilt and bitterness of knowing his status prevents that.
For me, this comes back to the question of how critics think Cat should ideally have treated Jon in an un-ideal world. How much could she or should she have changed things for Jon? He would still be unable to inherit. His presence at table would still be an insult to royals. He'd still be viewed with suspicion by the Westerosi for his bad blood. Ned's faffing aboutmight
still have left him uncertain about his future. (To veer briefly off topic, if Cat and Jon had had a better relationship, Ned might have been better about giving Jon clear options for his future, but we don't know for certain, and that's really on Ned, not Cat.)
Would Jon's bitterness have been less if Cat had doted on him, or would it just have been different? Cat didn't make him a bastard or dictate what his bastard-status meant about his lot in life.