Here's the problem with things like this list. Yeah, if we had to create new teams out of Farm Systems then the Sox wouldn't have hitters. Fortunately, they just hired JD Drew for 5 years, Julio Lugo for 4, they have Crisp for 3 more (and an option for the 4th), Wily Mo Pena for 2 more seasons (also due for an extension if he plays well this year), Youkilis under Sox control for 4 seasons, Pedroia for like 6 (he has less than a year of ML service) and Ortiz until 2011. That's 7 guys who could potentially be MLB caliber for the next 5 years. By then? I don't know, but the qualifier above was "Jacoby Ellsbury is the only star-potential hitter who is close". In 5 years those "non-close" people will be quite close indeed. Combine that with a FO that has had 2 of the best drafts recently and have money to spend, and I'm not really too concerned with the Sox offensive ranking.
I think the Yankees are largely in the same situation, though they have less of their future solidified--especially if A-Rod is a questionmark. you have to figure Jeter and Cano are here to stay, Damon will be around for a few years and I could see him signing a Berniesque extension. Otherwise, I'm vexed.
That said, I think the Sox and Yanks both approach drafts with a pitching heavy approach and I think that's a great way to do it. Look at the immediate impact that guys like Hudson, Zito and Mulder had on an otherwise weak A's team. I don't think there's anything wrong with havin gthe #7 ranked pitching system. Not only has some of that already paid off (Jon Papelbon) but other parts of it are close (Hansen, Lester, Delcarmen) and other parts are between 2-3 years away (Buchholz, Bard, Bowden).
If the Sox traded away two marquee players like Randy Johnson and Gary Sheffield they could get some great prospects too. What they couldn't get and didn't get were great major league players, and that's what ultimately matters.