I don't get it either. Even if you take budget constraints into account, Shapiro has never had a top farm system even after his promotion to president (which still looks fishy as **** considering he got promoted when Cleveland was .400).
Shapiro's drafting ability has always been a huge weakness. Only recently has that improved, and that may be because Antonetti gained more control over the draft, or once he relinquished the day to day operations of the club was able to put together better drafting strategies.
However he was arguably the best in baseball at stealing prospects from other teams.
He turned Bartolo Colon into Sizemore, Lee, and Phillips.
He turned Ryan Drese into Travis Hafner.
He turned Jake Westbrook into Corey Kluber.
The returns for Victor Martinez, C.C. Sabathia, and Cliff Lee were definitely underwhelming, but he still got an all star back in two of those trades as well as a solid number 2/3 starter in the other (Brantley, Masterson, and Carrasco) as well as some of the top prospects in baseball at the time in Matt LaPorta (who was a giant bust) and Jason Knapp (career derailed by injury).
Its easy to say the team wasn't very good after winning the 2007 division title, but you have to remember that he was squeezed by ownership into trading away the reigning Cy Young award winner two years in a row, and even in spite of that, the team was still poised to contend for the next 5 seasons however their top two players had their careers ruined by injury.
Think of how good the Jays would be if they were forced to trade away their top two pitchers and Bautista/Donaldson just woke up one day and couldn't play baseball properly anymore because of injury? That's what happened after 2007 to Cleveland.