When Rogers told Ricciardi to spend money, he signed Burnett, Ryan, and Molina. The only prospects he traded were Zach Jackson (ranked 6th in Jays system by Sickels in 2005) and Gross (ranked 12th by Sickels in 2005). He traded Hudson for Glaus (Hill outperformed Hudson that year so it was a great trade), and Bush for Overbay (poor trade since Bush way outperformed Overbay). Regardless, JP did not trade his best prospects. Unfortunately JPR could not draft very well so his best prospects were middling anyway, but still. He could have traded Rios, McGowan, League, and some of the upside talent he inherited, but he didn't. AA went the exact opposite direction. He could have swallowed up Santana's contract like the Royals did ($13m) but chose not to. He could have signed Bartolo Colon who signed with Oakland for peanuts after his suspension. He could have done a lot of things that didn't involve gutting the farm. He didn't have to sign the best FA's out there, just load the team with vets that could improve short-term and then letting the youngsters put them over the top in the years following.
JP as GM and AA's scouting team handling the farm system would have saved this organization. Unfortunately, the Jays couldn't combine the two aspects.