Why the CN would want the EJ&E is beyond me anyway. They are not going to gain any time bypassing the city using a painfully slow EJ&E. Crossing the busy UP/Metra lines at Barrington and West Chicago, plus the fact that double tracking would be nearly impossible for most of the route, the ROW is not wide enough. Metra wants the route for a new commuter line, but does not have enough equipment to satisfy current operations, they are objecting to the sale.
The only possible western bypass would be Madison, WI- Rockford, IL- Davis Jct- Rochelle- BNSF to Shabbona- UP to Troy Grove- NS through Hennepin then East. Sounds a bit silly, but at one time so did Rochelle intermodal site.
As slow as operations are now to get through the city a far western bypass is not out of the question since the Chicago suburbs are nearing the Interstate 39 corrider already.
And if for some reason Chicago does get the Olympics in 2016 there will be tremendous pressure on the railroads to route away from the city. Especially the CN(IC) which runs directly under McCormick Place and along the Lakefront with Olympic village. No ethanol trains wanted in that area. Lots of NIMBYS will surface.