Typically the inbound trains were full by the time they reached the Chicago city limits, which is Evanston. Historically there were only three stops within the City, now 4 (unless I'm forgetting some). Part of the reasoning for extending Metra to Milwaukee was for commuting within Wisconsin as well as general connectivity from the lakefront cities both north and south.
There were, historically, more stations both in Chicago and Evanston that C&NW ultimately abandoned. (Including a cemetery stop at the huge Roseland location, for funeral trains.) Ravenswood, now one of the most heavily trafficked stations on the entire Metra system (with a recently opened super wide inbound platform to prove it) was, decades ago, in an area becoming fairly downtrodden. It had, once, been a vital center of small manufacturing businesses as well as right next to a large Sears store. As such, it served a significant job core. But, with this all in decline, C&NW wanted to eliminate that stop, also. (Really, they wanted to eliminate about all of their in city service, except to the far northwest side, where they still had an exclusive market until what is now known as the Blue Line L got extended past Logan Square to Jefferson Park and O'Hare airport.). North shore residents of means, however, objected, as this (along with Rogers Park) were the stops many of their cleaning ladies used to get from the city to their houses. As such, this early form of reverse commuting saved these in city stations; stops which contributed to the eventual economic revival of the now regentrified neighborhood of Ravenswood, especially.
To tie the post back into the topic of a possible alternate route Chicago - Milwaukee, and what intermediate stops would be most desirable on either the current or another routing, I suppose it wouldn't necessarily require making all stops, if on what is now Union Pacific. Key traffic drivers for commuters could be chosen, with the opportunity to transfer to local service trains or other transit options, once in the Chicago burbs and city. Though, without adequate express tracks along the entire route, it would have to find the right slots to do so. Removal of one express track on the in city embankment (as part of a bridge rebuilding project and track realignment a couple of decades back) raised these concerns from a few well known (but often perceived as outlier) rail advocates. With changes in even local services from downtown oriented to local commuting, that concern about abandoned capacity is now showing itself to have been of importance.