Isn't the Chuo Shinkansen expected to have less capacity than the regular Shinkansen lines? I think the point that they'd be better off digging their tunnel and then running normal trains in it still stands. You'd still get a speed increase just by virtue of having a tunnel underground that takes a straighter path between cities.

As a side note (and I'm not counting this as an argument against the Chuo Shinkansen since it's my speculation): Japan's maglev technology uses large amounts of liquid helium and liquid nitrogen in the trains. I'm sure they've thought about this already, but there's a massive safety hazard if the cryogenic liquid leaks out because it will instantly turn to gas, displace all the oxygen in the enclosed tunnel, and pose a suffocation risk. They probably have some insanely complicated and expensive system to keep the inside of the cabin oxygenated if that does happen, which could have been avoided with normal trains.