I love you all the more for your faults.

Literal

I [topic-は] you [subject-が] flaws [object-を] having [reason-ので], all-the-more am-loving.

なおいっそう ('all the more') intensifies the feeling. 欠点を持っている ('having flaws'). ので ('because') marks the reason — the faults are the reason for greater love, not less. A beautiful paradox of acceptance.