Yes, Beane calls in the picks, but it's hard for me to believe he does so in a vacuum, or that he would consistently go against his management/coaching team's consensus to make questionable picks. I think he's smart enough to know that's not where you micromanage.
But it is his management/coaching team, and if they are collectively so ineffective at picking impact players in the early rounds, then maybe it is time for him to go. It's too bad, because I think he's a top-notch GM who has made a lot of bold and beneficial moves over the years. He just doesn't have the right team advising him on players and scouting.