It's a combination of the characters being memorable, the writing and especially the amount of choices I think that really makes it stand out. I play a lot of visual novels and I keep finding myself thinking "Yearning did it better..."
I haven't played in a while and still keep thinking of this game, so that says a lot about its quality. Oddly, Dan(the guy I initially ignored on my first playthrough) comes to mind the most when I think about the game. His writing was especially memorable and well done.
Anyway, I think I'll give Jame's route one more try. That is one elusive man. I just wanted to post this since I keep comparing games I play to it. Thanks for that, lol.