Drafting is definitely Rizzo's strength. He was with the organization from 2006-2008 as Assistant GM and VP Baseball Operations, so he certainly had a say in those weaker years, but he didn't get full control of the drafting until 2009. Along with signing top round talent later in the draft, it seems like he has also done a very good job of drafting in the middle rounds, something Bowden did not do very well at all.
The farm system is slowly being rebuilt. There is a lot of talent at Potomac and Hagerstown has become a juggernaut in the Sally League this year, but my thinking is that the organization is still about 2 drafts away from being well stocked at every level. Rebuilding the farm system is obviously one key, but a lot also depends on what kind of moves they make with that talent in the future. Rizzo hasn't had much success in trades to this point, but he also hasn't had a great deal of flexibility in terms of the talent he could offer. One would hope that he can make some nice moves as talent moves up to the AA and AAA levels.