I don't think, his father issues are anything liek you describe, sorry. He hasn't seen his father for a while, did leave him on a bad note and now his father is in danger. Of all the things, that can be critizised, this is not one. You can have a heroic independant life and still be worried about your parents. Maybe the Tiamat thing was a ruse by Mizora - Wyll wouldn't know and Mizora wouldn't tell. I don't see a problem.
You asked what can be done to make Wyll more popular. This is what I think would help. Well, it's not much help - "re-write everything" - but these are my problems with him. Do not think I am unique, there can be more people with such a view.
You certainly can be an independent heroic person and care about your parents. But Wyll's story is all about that worry. There is no heroic independent Wyll in the game with a grand life-changing quest. Only a boy worrying about his dad's approval. And even in this regard, he does nothing interesting and worthy of note. He is not a hero.
They talk about a dashing warlock but present a softly-spoken priest of a peaceful benevolent god. Nothing wrong with either of the concepts but they do not mix well. The result is so contrived it is hard to deal with.
I don't think, he needs a rewrite, he needs more content. People will always go for the flashy characters and not the morally good. Maybe give some examples of what you would like Wyll to do. 'Re-write everything' is not helpful. That is, what I would write for Halsin (better write him out), but that is not really helping. I'm not vibing with Halsin, so I have no idea, what to do with him, maybe it is the same with you and Wyll?
"We are all stories in the end. Just make it a good one."
