As far as Kaneko's designs I think the "sweet spot" for me was SMT II and Persona's 1/2.
Looking at the designs Kaneko created for the MC of SMT II it tells a lot about how he envisioned the setting alongside the character's design.
Aleph is initially living in the slums of a post apocolyptic world where people like him fight for the right to move into the higher class city called Center. His equipment looks appropriate for this type of background, it looks worn but functional and he's got a very serious look on his face.
Contrast this with his later reinterpretation of Aleph.
This new aleph doesn't really look like a warrior from a post apocolyptic work what with how form fitting and stylized his clothing are. The redesign suffers from a lot of minor gripes I have with Kaneko's later designs for humans. Like DukeMagus pointed out his later designs have this porcelain skin to them and in addition to that the eyes are vacant and overall the face looks pretty lifeless. This worked well in Digital Devil Saga and for the Mannequins in Nocturne but not so much for other games.