Your claims didn't match my recollection, so I just looked up a one-way fare from Tokyo to Osaka (6/25/2015; date randomly chosen) on the train, and on Kayak. The first train I found (not necessarily the cheapest) was $117 USD, vs. a cheapest airfare that was $55-$140 via the deep-discount airlines and $200+ for the less crappy ones. So yes, if you're willing to fly the discount airlines, you can save about $60.

That said, flying takes 1h30, plus an hour on each end, give or take, and then you have to get to the city. The train takes 170 minutes (~3 hours), doesn't require security, and drops you right in the center of town. That seems pretty competitive to me -- which is probably why most trains I've taken in Japan have been at least half full, and popular routes sell out on a regular basis.

I won't dispute that Japan has spent a great deal on their train system. The US has easily spent hundreds of billions on the highway system. It's a matter of priorities.

> So yes, if you're willing to fly the discount airlines, you can save about $60.

The point is that Shinkansen never offers discounts. The price is always the same. So if you are poor or if your company asks you to travel for business on the cheap, they will save on the trips using airlines instead of trains, because there is virtually no difference between ANA and any other discount airline for such short distances.

> That said, flying takes 1h30, plus an hour on each end, give or take, and then you have to get to the city

The Shinkansen arrived either in Shinagawa or Tokyo, which may be far from where you want to go as well. Let's not assume that "in the city" is close to your actual destination. Most of the time I need to take subway/train for another 30-40 mins so I'd say it's about the same with the plane. And security checks in Japan for domestic travel is very, very fast.

Even if you need to get to the other side of Tokyo, it's better to start from Tokyo station than Haneda (or far worse, Narita).

But like I said: trains don't have security checks, or the 2+ hours of boarding/taxiing/waiting that come with any commercial flight. A three-hour train ride is...three hours. A three-hour flight will take half of your day (at least), and then you have to get from the airport to your actual destination.

For a journey from Tokyo to Osaka, I'd have to be pretty cash-strapped to prefer a flight simply because it was $50 cheaper than the train.

Trains in Japan you mean. When I travel bullet train in China, the station is far away (often outside the city, at least on the other side of town), there are security checks, and I get there a couple of hours early just in case. Then I am on the train for 8 hours vs. a 3 hour plane trip (but can get off at my wife's hometown directly, so we still save time).

I agree that the Shinkansen can be regarded as a competitive option for medium-distance inter-city travel, but I think that daily use of trains in Japan can be expensive. A Tokyo Metropolitan pass costs 750 yen/day, and that's only sufficient if you don't travel outside the metropolitan area. In contrast, I only pay $5.50 round trip going between Evanston and Chicago on the L. Although I guess that comparison had more impact when the exchange rate was worse.

The airport in Tokyo was an hour to our hotel. I remember the Shinkansen being close to the hotel. We took it to Kyoto then to Osaka. The train was packed so even if it was expensive, it was full.

If you go during the tourist season, it's very likely full. If you go during early morning or evenings, they are likely to be full as well for people who do daily trips. During day-time, Shinkansen are half-full or even less that that. And I am assuming you had a JR pass, which means you had to seat with the "reservation free seats" which are usually always pretty much full and do not reflect the actual situation of the other wagons.

We had a reservation. Almost everyone else was Japanese, not foreign tourists

You probably flew out of Narita. Haneda is 20 minutes.