Yeah but the point is so does the train, and the train is arguably easier in between. It's a relatively short transfer from Haneda to the shinkansen, then just relax for a while and you're there. By plane, you have to take another flight (and I'm not sure about Haneda but at Narita we had to go through security again) and then a fairly long bus ride, both of which are physically more tiring. At Haneda, don't you even have to change terminals? Or are there domestic connections out of the international terminal?

I thought I might have been just remembering the bus ride as long but I looked it up and it is an hour - it's not just a quick hop. I dunno, for me after a total of probably 15-16 hours on two different planes, that's just a lot to ask. Overall I think the train is about even in terms of speed vs. the flight/bus combo, and it's definitely more pleasant. (I have done Tokyo-Kyoto separately by train several times.)

You can always take a taxi to the shinkansen to avoid the rush hour on the keikyu line.