Vaan is very important to the story. "To not have a character like Vaan existing is to erase the most crucial part of a story about people just to focus on power. That is to say, to craft a story with no context, to frame the people that populates the country as nothing more than a prop"
Understanding Vaan: a story of forgiveness and purpose - Dreamboum (very good read if you are interested in why Vaan is a great protagonist)

I think a big reason for why this is, is because Vaan was supposed to have a bigger role before that got cut, arguably penelope never had a reason to be through any of the events at all, she didn't care about revenge agaisn't the Empire, Vaan did, also the party doesn't work under the resistance just with them, they honestly have less reason to exist after the 2nd time the party is on the fleet

They could have just cast Vaan and Penelo aside after Bhujerba events, since Vaan proved to be too careless for exposing their identity. The resistance needed all help they could find but should have alocated Vaan to smaller tasks, keep working in Rabanastre under Old Dalan or something. But for the course of events to follow the main plot as it went, the group should have had a better reason to keep Vaan like an exceptional combat capability or unique role such as Balthier strategy or Fran knowledge. Honestly, deep inside they just wanted the fun guy to tag along

He may be useless to the Story perhaps but hes the strongest character in your party if build right so yea :D

One thought though, if it wasn't for Vaan Balthier and Fran would have taken the stone and probably not run into Amelia. Meaning She would have been captured. He may be irrelevant to the plot but without him the plot would have stopped in the first 3 hours of game play.