After having just used the JR Pass for the first time, my biggest gripe is the necessity to pass through the non-automatic gates. If only it could be preloaded into an IC card - such as Suica...
(naturally, a tangible ticket would still be needed for shinkansen/other trains, though why can't conductors just scan one's Suica/IC card to suss out the seat number/train name? Perhaps that's putting far too much confidence in the user.)