。
The problem is time, rather than cost.
Literal
Problem [topic-は] cost [than-よりも] rather time [copula-だ].
~より(も)むしろ ('rather than X, it's Y') is the standard pattern for correcting a presupposition or shifting emphasis. むしろ ('rather, instead, in fact') is the key adverb signaling the shift. より marks the item being displaced, よりも adds extra emphasis.