Saying it's an afterthought is a real disservice to how SMT games are written. It kinda saddens me to see people equate narratives which aren't dramatic or entirely focused on the linear path as "boring" or "afterthoughts". There's a lot of effort put into creating an interesting setting, and there are many characters and events which serve to flesh out the setting in various ways. Not everything is connected to the main quest lines, but almost everything you experience is relevant in some ways and can be pieced together to create a better understanding of the state of the world, what is happening in various places, how different factions and events are affecting the people who live in the world, and so on. There's so much flavor to be found all over, from the background design, the NPC dialogues, the item descriptions, and all the optional quests. There's always something there which makes the experience deeper.
How much plot you find and appreciate depends on how much you care to look. It doesn't mean they don't care about the story, it's just a different style of storytelling. Being subtle is one of the hallmarks of SMT, where the player is meant to be an observer who takes everything in while going about doing what he's required to do to survive. Along the way he will encounter various viewpoints, and decide what sort of future he favors for the world. The beauty is in how everything is placed throughout the game for you to discover and experience, and not thrown in your face with dramatic cutscenes and emotional events.