One issue with PCB is that it lacks the ability to do backannotation into gschem. That is, it would be nice if one could make small changes in the layout (e.g. pin swapping), and then be able to run a program (called "gbackanno", say) which would read the .pcb file & the .sch file, and then output a .sch file which wrote the new connectivity info into the .sch file.
-Dave