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Vargas was a 2nd-round draft pick, #68 overall. In fact, here's the list from the 2nd round in 2004:
64. Hunter Pence
65. Dustin Pedroia
66. Grant Johnson RHP, Cubs, bust
67. Kurt Suzuki
68. Jason Vargas
He was only a trade throw-in because of injuries, not because he was never considered a guy with a chance. He even got a Rookie of the Year vote in 2005.
In that regard he's more like Paul Abbott (one of my all-time favorites) -- who was a 3rd-round pick and in the majors at 22 (just like Vargas was) before heading to the scrap heap and resurfacing at 30 as a solid MOR starter.