I for one think the St. Charles Air Line should be used as the southward extension of the Clinton subway or else some other CTA rail project. I'm glad that the CREATE Grand Crossing project puts Amtrak and HSR on the NS line, since that leaves the SCAL open for such conversion.
Heavy rail trains can climb steeper grades, so climbing over the RI line and then descending back down to the level of the SCAL bridge should be a complete non-issue.
Put a transfer station for Red Line and Rock Island metra lines near 16th & Clark. Put another transfer station for Green and Orange at 16th & Wabash (This would be instead of the Green Line station at 18th that has been bandied about.) This transfer station would involve substantial reconstruction of the el in the south loop in order to fit in all the turnouts plus a platform and still be able to reach the ramp down to the State Street subway, but it MIGHT be possible. Something like
this.