Even accounting only 4 possible bodies (as in the Jupiter system) if 140 fly-bys are to be designed (as was the case for this particular mission) and at each fly-by one has to choose to "perform experiment" in of 1 out of 32 areas of the moon/planet, you have (4*32)^140 = 10^(295) possibile routes that all need to be optimized in low-thrust. It does not seem likely a computer will ever be built that can do that.