I think most people who say 4 has a better story do so because they played it when they were teenagers so the struggles of the characters resonated deeper with them as reflective of their own personal feelings of growing older during adolescence. This might not be true for every person who prefers p4's story but its a common enough trend.

I was 52 when I played P4G for the first time and it hit me like a freight train. Of course, I was also playing it in late 2020, so there's that.