Looking through all of the players JR has traded with the Penguins, who all has done better after leaving the Penguins? Despres is the obvious one, but beyond that? Perron had that hot streak that Hagelin also had to end 2016, but he put up around what he did with the Penguins last season with the Blues. Goc and Spaling are out of the NHL. Neal was over a PPG wing in his last season in Pittsburgh, followed that up with 3 seasons of a sub-60 point pace (2 seasons with a sub-50 point pace). Scuderi is out of the NHL at this point, but he also sucked when JR traded him. Bennett didn't hit 20 points last year despite playing in 65 games. Sutter is Sutter, he traded him before he started making a lot more money than he deserved. Plotnikov sucked in the NHL anyway, but he continued to suck and now he's back in the KHL. Harrington can't stick in the NHL and is now on his 3rd team.
You could say the same about letting players walk as free agents too. Comeau was a half PPG player in his season with Pittsburgh, he put up 20 points in 77 games last year (he did have a good 15-16 though). Downie put up a respectable 28 points in 72 games in his season here, he only played in 26 games with the Coyotes after leaving the Penguins before not playing in the NHL again. Paul Martin, you saw what age has done to Paul Martin in the 2016 finals. He let Lovejoy walk after the 2016 cup run, he faceplanted in New Jersey last year.
So with all of that in mind, what sort of reason do we have for questioning JR's decision making skills when it comes to letting players go? Because he's been almost unquestionably perfect when making those decisions. Why should we assume that him letting Bonino and Sundqvist go was the wrong decision? You could also include Daley in that group, because people have been complaining that the Penguins let Daley go and signed Hunwick to replace him.