I think Cherington has done a terrific job at building up the P prospect pool in his time here, both of the Pirates aces of the future in Jones and Skenes were Cherington picks and they have numerous other good pitching options that he has acquired or drafted. However, the bats have simply been neglected where Cherington has acquired very little bats to actually help out the major league team. Beyond Suwinski, who has his own issues, what exactly is there that Cherington has added?
The team is simply going to have to sacrifice some of their SP depth to improve the bats. If they're not willing to do that, nothing is going to change with the team. They have their top of the rotation for the next 5+ years set up with Skenes, Jones and Keller, but they simply need to help out the bats. Reynolds, Cruz and Hayes simply isn't enough and the development of their top hitting prospects (notably Endy, Gonzales, Peguero and Davis) has been a huge problem. I think Cruz is borderline in his development being a problem too, he's still a good player but he doesn't look like he'll end up close to the sky high upside his physical tools suggest.
To me, the Pirates have Cruz (leadoff hitter, SS), Reynolds (#3 hitter, LF/DH) and Hayes (#6 hitter, 3B) sorted out. I also figure Endy's defense will make him a sufficient starting C as well, with where he falls in the batting order dependent on how well he hits. Beyond that? It's really not encouraging. They have glaring holes long term at 1B, CF and RF that Cherington seems intent on doing nothing about. The dumpster diving every year for 1Bs just shows that.