I'm not sure where you are planning for this to go but I do have a kind of idea for what I would like to do with Amelia.

I do want her to stay on the ship for the length of the story. I want to use her as a symbolical character as well as create a bit more tension. To Daniel, Avery is everything new/adventurous/wild/world savy where as I want to put Amelia in a position where she is everything old/what he had first dreamed of/docile/wide eyed innocent. I am planning to have Amelia fall for the doctor, and kind of be his good temptation to choose the life he wanted as a child. Avery would be his choice for life on the sea (which he will ultimately choose). I think it would toss in an interesting dynamic. Maybe Scarlet and Amelia can become good friends during the adventure?

Also, what I just said may make more sense if I explain what I'm thinking for their ages (please correct me if i'm wrong). 
To me; Avery and Daniel are within 2 years of each other, Bane and Avery/Daniel are within 5 years of each other with Bane being older than the two, Amelia is 4-10 years younger than Avery and Daniel. I don't know the average age for pirates and the like so this is just a rough idea of the potential gaps between the characters.

[@MegaraFoxfire]