The Main Character Throughline
The Main Character Throughline is perhaps the hardest for any writer to address in their story. Why? Because it's much easier to write about other people's problems, than to explore the personal issues one experiences deep within. And make no mistake, almost all Main Characters are proxies for the writer themselves.
Writing the Main Character Throughline should be uncomfortable for you. The more truthful you are in exploring those personal issues that you alone experience, the more readily the Audience will empathize with your story's narrative.
Many writers conflate the Main Character Throughline with the Protagonist of the Objective Story Throughline. And even if the Player representing the Main Character is the Protagonist (a Hero), they will still possess a set of narrative dynamics that are theirs, and theirs alone.
The thematic material in the Main Character Throughline should be that baggage that the Main Character would take with them into any story. You want to write something universal, regardless of situation, something the Audience can look at and say, Oh, I remember being that way or I remember feeling that way. The only way you can do that is by writing the Main Character Throughline in isolation.
Try your hardest to illustrate this Throughline without thinking of your Objective Story Throughline. Do it on a different day if you have to, whatever it takes to get into the headspace of someone dealing with initimate personal issues.