I think it would be more expedient to route through trains over the St. Charles airline connection and have them continue through Union Station to points north and northwest of Chicago. The Interlocking at Western Ave. could be rebuilt with or without flyovers to allow for faster operation when trains switch to and from the ex-CNW line to the west and when they cross over to continue to Milwaukee.
Ideally, there would be new construction to combine Olgivie and Union Station to create a superstation that would provide easy connections between the platforms in Oglivie and the platforms at Union Station. This concourse would be above the tracks and below the street level. It would have shops and restaurants. If this was not possible, then there should at least be escalators at the north end of the odd number platforms to facilitate getting to Olgivie.
Run-through operations should be emphasized at Union Station. The ultimate goal should be 30-minute off-peak service on all metra lines. This could be accomplished with new equipment based on what is used over in Europe or Japan. The RER network in Paris is a good blueprint as well as the Elizabeth Line and Thameslink in London.
At Ohare, the people mover would need to be extended to the Metra station. Some sort of route would also need to be built to get people from Union Station to Midway airport.