I think the reason a hsr line like this does not exist for these routes is simply because the monetary demand/value isn't there.
Going from Tokyo to Kyoto and back is probably the single most used rail line on the planet in terms of value. That one line is enough to drive an impressive chunk of the entire nation of Japan's economy. And along the way on that route, there are tons of other slightly-smaller cities that make the route extremely efficient.
But Chicago to Madison, Chicago to Milwaukee? There just isn't enough value there. Anyone who WANTS to get from Chicago to any of those places on rare occasion can just drive (the US beats probably everyone else, certainly Japan, at that). Anyone who NEEDS to get from Chicago to those places can fly or take the slow train. And that route is not powering a significant portion of the US economy, like the Kyoto-Tokyo route. And besides some suburbs, there's really nothing along those lines to make them efficient. It would be billions of dollars invested to get people from Chicago to a cities that aren't very important to Chicago. And if any of those cities start to fail, that line is basically useless now, since there's nothing else along it, it only goes to one place.
The problem is in the layout, really -- the economy is powered by New York to Chicago, Chicago to LA, Dallas to Seattle, etc. And these are distances where a plane is going to give you advantages over high speed rail -- ESPECIALLY considering there is basically a whole bunch of nothing between the cities, as opposed to the unending line of coastal cities that live along the Kyoto-Tokyo line.
One look at a population density map shows exactly why Japan's rail line is so highly efficient: http://www.mappi.net/japon_densite.gif
You could draw a straight line that goes through 99% of Japan's population. And that's exactly what they did, but with a railway.
I know I didn't talk about Europe here, but I don't know much about Europe. Though my rough understanding of European geography tells me that it is also more efficiently organized than the US, and therefore also more suited for HSR.