Advantages:
Better sealing properties, more precise location and exact compression af sealing material, utilization of other, more suitable sealing and spezialized sealing material (O-rings).
Disadvantages:
Commercial availabillity and cost. Normal raised faced is far more common and ready available both regarding Valves, flanges and sealing material. Another complexity is that some rigid rules must be applied to the piping design. Do you order Valves to be female end both sides, or on one side maybe, in which case do you point all male ends in the flow direction, or what. Same applies to any flanged joint / vessel connection of course.