Cloverleaf intersections have really poor overload behavior. They're fine in low traffic areas, but in places with high traffic, the crossing streams of traffic

Cloverleaf intersections have really poor overload behavior. They're fine in low traffic areas, but in places with high traffic, the crossing streams of traffic cause cascading backups. Stack interchanges increase acheivable throughput because you can often build enough road to allow backups for one direction to not impinge on the other flows. It's also easier to build effective signage so there's fewer surprise lane changes.