What's at issue is not his ability but his personality.
Literal
Problem [to-と] has-become [nom-の] [topic-は], his [poss-の] ability [not-ではなく] personality [copula-だ].
Uses ~となっている (formal 'has become') and のは (nominalizer + topic). となる is the formal equivalent of になる, lending the sentence the feel of an executive summary or assessment.