I think anyone who classifies JRPGs are linear, un-customizable single-route stories that feature annoying whiny characters with slow turn-based combat should play Shin Megami Tensei Nocturne.
Nocturne isn't perfect by any stretch of the imagination, but it does feature a very deep world despite having a very low character count. It has a morality system of sorts that effects the ending, but the various ending are all varied and aren't just your standard "good, evil, neutral" endings. The combat does feature random encounters and turn-based combat, but Atlus is awesome at taking turn-based combat and making it into something that keeps you on the edge of your seat. Also, each encounter is practically like a puzzle, which keeps all battles interesting.