I think that the actual significance of this game being a hit is showing that there's a market for JRPG gameplay divorced from JRPG storytelling.
JRPGs as they currently exist are kind of an interactive extension of the anime industry. There's subtle differences, but not enough to differentiate the audiences much. And that's fine, anime is a growing medium and people like the games that are getting made. But there's a huge audience of people who play video games who aren't gonna show up for coming of age stories about ridiculously clothed teens with technicolor hair, high pitched voices, poor communication skills etc.
It's incredibly healthy for the gameplay structure to be divorced from the art and storytelling expectations that have gotten so entrenched. There's no reason for them to have to be a package deal. Games like Expedition 33 will lead to a wider audience playing this style of game, which will lead to more and different developers taking chances making these games, which leads to a more diverse and vibrant scene overall.
Meanwhile Atlus will continue making Persona "my self insert high school anime fantasy" and Square Enix will continue making Kingdom Hearts games about the power of friendship and light overcoming darkness. Falcom will never make a game about a character older than 19. The games that were already getting made are not at all under threat, there's no downside.