An $8 billion "really outer" beltway is being proposed to handle trains running through, instead of to, the Chicago area. It should reduce the transit time from 30 to 8 hours.
The Tribune article indicates that Union Pacific would be unwilling to use the new bypass. One comment I saw indicates it is because they don't want to short haul their traffic. That is, they don't want to reduce the mileage they get paid for by about 50 miles. I presume another reason is that they don't want to share the revenues with another party. (UP owns part of some of the other belt railways so they would get part of the interchange fees.)
In addition to the CREATE program inprovements, Canadian National continues improving the Elgin, Joliet and Eastern (EJ&E) that it bought from United States Steel to bypass Chicago.
Furthermore, a lot of the congestion is going to fix itself because of reduced rail traffic. Coal cars and fracing sand cars are already setting on storage tracks rather than rolling through Chicago. The bigger Panama Canal should reduce the container trains from the west coast to eastern cities.
So by the time a super bypass processes EPA and regulatory studies and is built, the congestion in the Chicagoland area may already be gone.
Update: people didn't want their rural life disturbed by a railroad, so let's tear up the land with a railroad, tollroad and a South Suburban Airport. A new expressway was proposed, but it was shot down by a governor. Before that, a new airport was proposed down by Peotone, IL. Some government agency had already bought a lot of land for that, but it was shot down. And every time I drive by that I-57 exit, I'm glad I don't have to drive that far just to pick someone up from the airport. Since then they have bought more land at O'Hare and built more east/west runways. But they never did get the planned west entrance built.