Why then don't aircraft fly even higher, for even greater efficiency?
Some do (or have in the past) but very high altitudes present their own issues. Historically the Concorde cruised anywhere from FL550 to FL600 and was actually allowed to climb and descend at its discretion up there since they were well clear of any traffic. However the increase in pressure differential on the airframe as well as supersonic flight meant the airframe saw much greater wear and tear per cycle than its lower altitude friends. 

At some point you get near the coffin corner a point at which, even if you have enough thrust your stall speed exceeds your critical mach number (effectively your wing can't work right). The U2 spy plane is capable of flying right on this edge.  

One of the big practical limiting factors is also the rapid descent requirement for airframe certification. The FAA requires that in the event of a depressurization the aircraft can get down to 10,000 ft. (no oxygen required altitude) in 10 minutes as discussed here. The higher you go the faster the emergency descent needs to be, eventually this becomes an engineering issue and the airframe becomes the limiting factor since you don't want to exceed Vne in the dive.