Can someone explain this to me, I have read it several times and feel as if I'm missing something.
I see, I think, what you would like explained. However, before I even begin, I need to be sure. So, I'll reword what I think you are asking:
"Why should a wife submit to her husband if his leadership skills - spiritual, economic, social, etc - are lacking to such an extent that it is obvious he has not earned that submission."
Is this a fair representation of what you're asking?