Okay, so I'd been avoiding Affinity Missions like the plague since I got one that forced me to go to Sylvalum when I'd only just reached Oblivia. (They really should have fixed this and not allowed you to join Affinity Quests you are not ready for, or at least let you back out of them)
Anyway, I finally got over my phobia and started doing them again, and now I see why I felt like the main plot was so thin; a lot of the character development is relegated to the Affinity Missions. Enjoying the game a lot more now.