1: Extend the south Chicago Green Line (Dark Green) down the Metra Electric's South Shore branch (via Light Green Line).
The Metra Electric's South Shore Branch gets three trains an hour during rush hours, one train an hour otherwise. Hooking up the South Shore Line with the Green Line would allow for an increase in service at least to three-four trains per hour during regular times, up to eight trains during rush hour, improving and integrating that area into the CTA rail system. Plus the additioin of the transfer station between the new green line and the Metra Electric allows for further integration of the system in a way that actually improves access on the south side. Plus you get three new docking spaces for South Shore service.
2: Extend the Red Line (dark red line) down the Metra Electric Main Line Local and Blue Island Line (via Light Red Line).
For this, I would rebuild the west two tracks of the Metra Electric into CTA tracks, complete with separate entrances and paying mechanisms. You'd also have to fill in space from the 111th street station to where the Blue Island Line turns off and build a transfer station system either at the 111th or 115th street station. However, such a system would improve Mass Transit Access to the Pullman areas and other areas south AND add three more lines for South Shore Service, should it be needed.
3: Rebuild the rest of the Metra Electric for separate local and express service, with the locals run by CTA equipment (the Gray
While there are questions which will need answering for the North End of this service, the portion from 95th Street north can be shifted over to CTA-type service. While I'd prefer the locals shifted over to the west tracks and the express kept of the east 2 tracks, the present alignment can be used as long as one can create a way to keep people from jumping services without paying. The express tracks can be made one-way boarding and unboarding (like King Drive on the Green Line's East 63rd Street branch). And unless the Gray Line ends (or continues through) the "Millenium Station" (formerly Randolph/Water Street), even more docking and parking spaces will be created for both the South Shore and Electric Lines to use.