Last year, it was Wiggins and a big ol' pile of hope. Their best pop-up pitching prospect (Gallagher) was traded, Mason McGwire was out with injury, Birdsell was freshly injured, and their only notable pitching picks in the draft (Reid/Wing/Coppola) were relative unknowns coming out of the draft. Go back and look at the forum this time a year ago; prospecteers and people on this forum were seriously trying to talk themselves into guys like Nick Dean and Connor Noland. It was horrendous.
This year, it is better, thanks in large part to the volume of picks spent on pitching compared to past seasons. You're correct that Wiggins was pushed down due to his injuries, but the guy is still going to be a fixture on every Cubs top 10 list in the offseason. Townsend is a known quantity and was a potential Top 10 pick before lingering injury issues pushed him to the Cubs, so he'll similarly feature on the lists, and you'll also see glowing writeups about guys like Jasa, Blomker, Meyer, and Alwood in the offseason around these parts if @Jason Ross needs material during the lockout. There also were notable steps forward from guys like Coppola and Caple, not to mention Wing (pre-injury) and McGwire (pre-trade).
Is the system a world-beater in terms of its pitching quality and depth? horsefeathers no. It's still bottom third in the league and has a long way to go before we can even consider the pitching to be mediocre. But that's better than being deadass last or second to last, like it was last season.