My first thought is that I disagree with comparing Jubilee and Vaan:

Jubilee had an important role in the story of the X-Men Animated Series, and she had established relationships with a majority of the cast and interacted with them on a regular basis.

Vaan was simply tacked on and had very little interaction with the rest of the cast and had very little relevance in the storyline, too.

As for Persona 3, I never finished the game, either, because of the reasons that you mentioned. I dislike the social aspect of the game, and I wish there was a way to play through it in a more linear fashion. The scenarios that occurred every couple of months which involved confronting a boss had my attention much more than the tedium of daily life in that game. I found it depressing to watch the calendar go from day to day.