Well, that is a different complaint than the one I quoted. I quoted you saying our system was weak because of some guy's ranking list and what players he had listed for some of the higher spots. I wasn't saying that there was no weakness in the farm system, just that the method you used to arrive at the conclusion that the farm is, overall, "weak", isn't a very good one.
It's true, most of the kids with better tools/talent are at lower, undeveloped levels. That's going to be the case following acquisitions of prime-time players like Gonzalez (and Victor Martinez only 1.5 years earlier), and deadline roster help like Bedard. I don't think it fair to demerit the system for lack of ready talent when the system has recently been used to subscribe to your preferred philosophy - that the ultimate value to the MLB team is to use their prospects to acquire stars (like Gonzalez and Martinez), or at least established veterans when there is need(like Bedard). If your point is that the farm should produce enough quality prospects to both land stars and provide ready talent to back up the big club, then I think you suffer from unrealistic expectations.
Also, I don't think the upper levels are as weak as you are suggesting. Alex Wilson is coming off a very solid year in AA/AAA and will start the year in the Pawtuckett rotation. Brentz is coming off a monster year in A/A+ and will start the year in the OF in Portland. These guys, Middlebrooks, Lavarnway, and Kalish are all realistic expectations of potential help if the big club needs help at their respective positions. Then, there's always to possibility of a highly regarded talent like Ranaudo, Iglesias, or even Tazawa showing improvement and being ready to contribute. I don't think it's anywhere near as dire as you are putting it.