There had been rumors floating around about this for a couple of weeks, but as the deadline for affiliation agreements to be renewed passed Monday, it was made official:
Much of the Cubs brass descended on Fifth Third Bank Ballpark during the season and in 2013, a nod to the convenient commute from Wrigley Field. Despite optimism from both sides – new Cougars owner Dr. Bob Froehlich and Cubs president of scouting and player development Jason McLeod both lauded the arrangement this summer – the Cougars enter an important week without a 2015 affiliation. Beginning today, major league teams can negotiate with unattached minor league clubs for two weeks. The Cubs’ decision to end their PDC with Short-A Boise and possibly do the same with Advanced-A Daytona has the Cougars and those in other MWL circles cognizant of a possible change. Per ballparkdigest.com, the Cougars, Beloit, Fort Wayne and South Bend are the lone MWL clubs that haven’t renewed PDCs. Each team in the corresponding Class-A South Atlantic League is attached to a PDC next season.
Beyond the fact that the Cougars have a strong brand that draws fans from a population base of over 600,000 people who live within a 30-minute drive of Geneva, and the fact that they've drawn Cubs fans to their park the last two years who might not have otherwise gone to a Cougars game, the affiliation makes sense from a baseball standpoint.
As noted in the link, it's easy for Cubs executives to drive to Geneva to watch their prospects in the Midwest League, something they've done often. It provides a convenient place for rehab assignments for injured Cubs, something done by Ryan Sweeney, Kyuji Fujikawa, Luis Valbuena, Rafael Dolis, Scott Baker and Shawn Camp over the last two years.
There doesn't seem to be any reason for the Cubs to change. The Cougars are embarking on an upgrade of their ballpark, both for fans and players; among the upgrades are batting cages and tunnels built to the Cubs' specifications:
On Sept. 2, the day after the regular season ended, the Cougars announced a capital improvement project for the 2015 season, the club’s 25th in Geneva. Construction projects include a high-definition video replay board, expanded weight room, advanced video room, new batting cage and climate-controlled hitting tunnels and a permanent music pavilion/concert area. The Cougars already have removed seats from behind home plate for a premium viewing area that includes wait service, and plan to begin concrete work on that phase next week.
Of the three other Midwest League cities looking for affiliates, none really makes any sense for the Cubs. Beloit has a facility that's not nearly as good as the one at Kane County is going to be; Fort Wayne is a three-hour drive from Chicago, one of the farthest Midwest League cities from Wrigley Field (you can see all of them on this map) and affiliating with Fort Wayne or South Bend would be "too much" for those teams, according to this Baseball America article.
The negotiating period between major-league clubs and unaffiliated teams goes through October 7. MLB and MiLB will match up any unmatched clubs after that date.
It's unlikely the Cubs would let that happen, though you never know. It really makes no sense at all for the Cubs to have an affiliate anywhere else in the Low-A Midwest League (and it would have to be in the Midwest League, as the affiliations in the other Low-A league, the South Atlantic League, are all locked up).
In the end, I suspect the Cubs will be back with the Cougars. If they do, I hope they sign a four-year deal instead of the two-year agreement that just expired; continuity would be a good thing for both the Cubs and Cougars.