There is less air friction if your tunnel is maintained at vacuum.
Indeed there is zero! Realistically speaking of course, a hard vacuum will be difficult. Even a 0.10 atmosphere would be a huge improvement. Or the intriguing possibility of pressurising but with a less dense gas. Helium, for example is about 1/10th the usual mix of gasses on earth. You could put a plastic sleeve over the shinkansen routes, fill it with helium, and see air resistance drop 90%. We might not actually have enough helium for that, though.
I'm just trying to say, there are options, if we truly care about speeding up point to point travel in-atmosphere.
Without even getting into problems that will occur at tectonic plate boundaries...
Not to downplay the size of the task, of course; it would be an astonishing feat of engineering and probably quite out of our reach for the foreseeable future, at any kind of reasonable cost anyway. The tectonic boundaries, as you say, would present a particularly challenging aspect of the project. However, theoretically it's probably the most efficient way from A to B on our little blue marble and so no doubt it'll be done eventually.
