I could be talking out of my ass, but I think they do it on purpose. P4 has every stereotype required for a JRPG cast: Goofy, hot headed sidekick, tomboy girl, quiet reserved girl, tough but soft guy, endearingly weird mascot character, overly moe girl, and the ultra serious plot device character.
But what they do is take all of those and really dig into why those archetypes exist. What makes those people tick and why they act the way they do. They even go into how they do not act how they're expected to. It's all a play on expectations, including yours as a player. I'm not going to sit here and say that the characters aren't archetypes because they absolutely are. It's the fact that we get an unusual amount of very relatable depth that makes it so satisfying. A lot of games have deep characters with well explained backstories and motivations, but rarely are they ever so intimate and easy to relate to. We may overhype it and inflate it in our minds (hindsight is usually positive leaning), but it definitely felt fresh at the time.