The problem is that because of the success seen by the Sox in the Mid-00's, they deemed it a good idea to start drafting high-upside HS talent thinking that the run of success was sustainable for a couple more years with what was the current core back then. The problem with that is that it takes a lot longer to develop, even though the payoff is usually much greater. That created a gap between the then current MLB-ready prospect crop and the next.
Don't be surprised if, in two or three years, guys like Bogaert, Jacobs and Barnes become high-production MLB players, making this current discussion seem a bit silly. The Sox farm system is very strong on talent, the problem being that it's very bottom-heavy.