The problem with party member quests will exist in any game where party members > party slots. Going from 4 to 6 mitigates that a bit, but it does not solve the underlying problem, which is that most games require you to have a party member in the party in order to do their quest.
This is really an arbitrary restriction and it seems like it would be fairly easy to lift. Just make up some handwaving BS about how only 4 people can fight at a time, but they are all with you. This isn't really any sillier than leaving multiple people in the camp. Realistically, if you have 9 powerful allies you would have them with you all the time, not just twiddling their thumbs in a camp.
All of these restrictions are arbitrary. Just balance encounters around N party members, and then lift the restrictions on requiring particular party members to be one of the N to complete their quest.
