Last time I was in Japan, a typhoon hit, and was working its way up the islands. My flight up to Tokyo was already cancelled due to high winds, but I was able to get a Shinkansen ticket and arrive in time to catch my flight before Narita was affected by the Typhoon.
The flight would have been 90 minutes (not including travel time to the airport), and the train was 5 hours, but still, it was a comfortable journey and I'd do it again. If I were traveling from downtown to downtown, the airplane time would be more like 4 hours (60 minutes to get to airport with padding to get to gate on time, 90 minute flight (scheduled time is over 2 hours, but usually the flight is around 90 minutes gate to gate), then at least 90 minutes to get off the plan and catch an express bus to Tokyo.