Are you looking to develop/refine one specific muscle/muscle group/set of muscles? Then isolation is your answer. Rehab from an injury? Isolation. Balancing asymmetric development...again isolation.
But if you're looking for total body health, fitness (aerobic, endurance, recovery), coordination or better kinesiology (how your body moves efficiently) then compound is the way to go.
Think of it this way: you got ONE body, everything's connected. Not very much in real life is a pure, isolated movement, why should your exercises be?