I'm going to guess that you're referring to the offline mode as story mode, but there is also a "story" in the online mode and the NPCs will change what little they have to say depending on events that occur as the result of succeeding at certain (generally the rank-up) quests. Unfortunately the vast majority of a hunter's time past the 50 hour mark will probably be post-ending where NPC blurbs become frozen and what little story there is is easily forgotten.
I would compare the structure more specifically to Phantasy Star Online. You have your hub, you pick a quest, and you and your party set out. Unlike PSO, there's no joining people midquest. Given that you could end up waiting 50 minutes for them to return, it would be nice if they fixed that (even just a spectator mode would be welcome).
It's a bigger game for sure, but Tri was, comparatively speaking, not that big on content.