A couple of really good prospects do not a good farm system make.
I'd argue that that is the better farm system than a bunch of decent prospects. I'd take a farm system that produces nothing but a Robinson Cano or Philip Hughes every 5 years, and I'll fill in the rest with replacement players. Better than getting a decent player every year but nothing significantly above replacement level (ahem, Youkilis, Pedroia). Sure it's nice to have diversification of the portfolio, but for a team like the Yanks, developing a superstar is more important than the issue of developing an average 2B who you have to pay minimum $300,000 rather than buying an average free agent 2B for $1 mill.
A recent column on the SI web site is meant to be humorous, but the writer makes some good points, including this:
Perhaps humorous, but wrong. Cano and Melky were International Free agents, but hardly big bonus guys. Anyone could have had them for a few thousand dollars. Wang is the only guy for whom the Yanks' coffers were an issue.