It is a known bug that FSX will route you from New York to London via the scenic western Canadian detour.  Co Pilot from Abacus will create a correct route, and so will FS Build.  But for default FSX planning, I use your method of creating a GPS route, then dragging the line to the waypoints.  It is tedious, but can result in a more realistic flight plan.  I put in a lot more than a couple, though.