The differences are indeed dramatic. However, clumsy control inputs are not something found at the highest levels of motorcycle racing. Not in the 50s', 60s', 70s', 80's, 90s' or today. So though it is true that being clumsy will quickly land you in the hay bales, it isn't anything that you'd of caught Agostini, Hailwood, Reed, Roberts, Sheen, Spencer, Gardner, Lawson, Rainey, Schwantz, Doohan, etc doing. Therefore, I still maintain that they would not be caught-out by the excellence of today's MotoGP bikes. In fact, it is my assertion that the mid-80s' through late 90s' riders dealt with by far the hardest to ride motorcycles ever produced for racing.
That said, I do think that Rossi is one of the all time motorcycle racing greats and perhaps "the best ever" -Sean