The current plan is to eventually run the Lincoln Service and Texas Eagle on the Rock Island Line using the unbuilt connection from Union Station yards to the St. Charles airline. The Rock Island line has too many grade crossings for high-speed running.
IMHO, the current route between Chicago and Joilet could be more easily improved by building flyovers over the diamond crossings that frequently delay current operations. Ideally, as soon as a Lincoln Service train turns after crossing the Chicago River, it should be able to accelerate to 79 mph and maintain that speed using the flyovers. Currently, the trains limp at about 30 mph until after crossing Pulaski west of the Corwith intermodal facility. After this, the train could accelerate to 110 mph and maintain that speed until a few miles out of Joilet. An additional flyover west of Summit is needed. These improvements, IMHO, could eliminate 30 minutes off of the travel time between Chicago and Joilet, a distance of 37 miles.
The segment from Alton to St. Louis currently has to contend with slow running through junctions south of the Alton station. Then, it runs at 79 mph until reaching the bridge over the Mississippi River. IMHO, 15 to 20 minutes might be removed from this running time by building flyovers over the junctions and allowing trains to run 79 mph all the way to the bridge.
There appears to be enough room south of the junctions to build separate tracks for Amtrak until reaching the bridge. If these tracks could be built to 110 mph capability, this would reduce the travel time and eliminate the need sometimes to send Amtrak over the slower Merchants Bridge route. Capacity improvements here and probably a few places between Alton and Joilet could allow for additional frequencies. This corridor really should have at least trains every two hours throughout the day.