Every GM, in hindsight, makes bad picks and bad trades. I think Beane generally does very well by the team, and the results speak for themselves. He is diligent and aggressive when it comes to filling needs. I think he listens to the coaches when it comes to draft picks. He is good with contracts - he gets team-friendly deals, and by and large, his best players really want to be in a Bills uniform.
His greatest sin as a GM was giving McDermott too many chances, but even that opinion is weighed by hindsight. I really think you have to judge a GM by the moves they make when they make them, not after the fact. On that basis, Beane is one of the best.