I don't mind the Cubs' meh middle minors depth, to be honest. It's not that I like it or anything, but, you can stock that part of the system reasonably well out of the draft. If the Cubs didn't trade Smith and Mathis had a healthy season, I get the sense there'd be less consternation over it. But, we at least have enviable depth in the low minors.
Actually, I'd be more worried if there the lower levels were empty, since part of what killed the farm post-Bryant were the trades for guys like Quintana and Chapman.
It's not a great place for the farm, but I think it's something that can be fixed much more easily than weaknesses elsewhere in the system.