The way I see it. O'Brien didn't care about the major league team last year. His main goal was to restructure the organization, bring in his own people, improve the minor league system. I think he did all three. I think the minor league system is improved although not top tier quite yet. The organization seems more professional. He signed lots of draft choices and seems to have drafted some good arms, although very young ones. On these tasks I would give him a B+.
However, the major league team was not improved. His acquisitions were the usual array of cast-offs and fringe veterans. He didn't trade off salaries (Graves, for example) that need to go. He did nothing to bring the Griffey situation to a head, and now Griffey has 10 and 5 rights. And when the team was competing, he didn't try to bolster it (except for Gabe White). On these tasks I would give him a D.
If he doesn't turn his attention to the major league team this off-season, I will be disappointed.