It appears that there is hope that they have turned a corner towards a brighter future.
According to MLBfarm.com, the Twins' minor league pitchers have allowed the second fewest earned runs (1,281) in baseball. This number is organizationally wide so, from top to bottom, there are some strong teams:
Rochester's staff (3.25 ERA) has the best ERA in the International League.
New Britain (3.98) is sixth out of the 12-team Eastern League.
Fort Myers (2.99) is third out of the 12-team Florida State League.
In ten games, short-season Elizabethton (2.11) is leading the Appy League.
Only Cedar Rapids in the Midwest League has been the only team in the system that has produced a below average ERA.
Yes, ERA is a poor stat to use when it comes to evaluating pitching overall -- what with the subjectivity of errors -- however, this goes to show that the system is fairly strong across the board when it comes to both pitching and defense.