If cross-country trains were a viable alternative I'd choose them over flying in a heartbeat.
Also the train was like 6 or 8 stopovers and changes. Absolute insanity.
In Japan they are still several times more expensive and slower (over long distance, as OP suggested).
And while this depends on the train service, the comfort is generally much better - there's more legroom and the seats are more comfortable, and if they serve food on board, it's superior to in-flight food. And that's not even mentioning other benefits like no limits on luggage weight or not having to throw out all drinks before boarding.