It doesn't take long for a farm system to turn around. A solid draft or a great trade can imbibe new blood into a system, just like a bad trade or graduating players can leave a system dry and underwhelming. For the Twins it seems they've always been a middle of the road minor league franchise, but over the last few years the trademark has changed.
For the longest time that trademark was pitching. Looking at the hurlers from the turn of the millenium, a vast majority of the staff not only came through the Minnesota farm system but they were good pitchers as well. A few years later another wave of pitchers came through. But we've seen very little since. Remnants of that last wave are still around, obviously: Scott Baker, Francisco Liriano, Nick Blackburn, Glen Perkins.
That was a wave we were excited about six years ago, and things have changed. There is no "next wave" of pitching on the horizon, only a player here or there. And the calling card of the system certianly isn't pitching.
On the plus side, the system is more balanced. Where years ago there were no position players of note on the rise, now our best prospects play anywhere but on the mound.
SB Nation's John Sickels recently rated the farm systems of Major League Baseball, and pplaced the Twins in the middle of the pack at number 17
Another middle of the pack organization, fairly balanced between hitting and pitching, some potential regulars with several solid role players.
ESPN's Keith Law ranked the Twins a bit higher (Insider required):
I pick on these guys for taking low-ceiling college arms with great control, but they have quietly mixed in some interesting high school bats and added a few high-impact Latin American prospects.
What's interesting is that although Minnesota is clearly a middle-of-the-road system as far as a couple of the game's more respected minor league analysts are concerned, they actually have the consensus second-best system in the AL Central. Nobody likes the White Sox minor league system (ranking dead last on both lists). Cleveland isn't much better; Detroit ranks just a tad higher. The Royals are ranked fifth (Law) and sixth (Sickels) on the two lists, and with good reason.