The other problem they had was, 2016 happened due, in part, to luck. The Cubs hit on multiple high quality prospects (Baez, Schwarber, Contreras, Almora), had a generational talent falling into their lap in the draft (Bryant), and won on trades that critically bolstered the team (Rizzo, Russell, and Hendricks). There was a bit of arrogance from the organization, like they could sustain this success and just have an assembly line farm system churning out one great player after the other.
However, while they deserve credit for identifying and developing those guys, they also got lucky. Schwarber was the only major injury to come out of that group in 2016, and he somehow managed to come back for the World Series. Everyone hit on the high end of their development curve. The Astros could have easily drafted Bryant over Appel.
Since then, most of their top flight prospects have suffered injury setbacks (Howard, Horton, Wicks, Marquez, Alzolay) and/or hit developmental brick walls (B. Little, Jensen, Lange, Howard and Marquez again). It seems like they've finally turned a corner, and they managed to develop solid pieces like Happ, Hoerner, Busch, and Steele in the interim, but it's taken nearly 8 years to get the farm to where they thought it would be.