All Bill James says is that WAR isn't a perfect stat, and everybody knew that. The article does point out that the MVP lately, since 2012, has the highest WAR from fangraphs. I like WAR, but I don't think it's perfect and would never follow it slavishly as the MVP voters seem to be doing.
And what I like about WAR is that it at least tries to combine all the attributes--offense and defense and baserunning--of a lineup player. I also like Ken Pomeroy's NCAA basketball statistics because they are pretty good. But Pomeroy is always tinkering with them based on new information and insights. One hopes that fangraphs has the same approach because combining attributes is tricky business.
On talksox, for example, we have a strong contingent of folks who believe that defense, especially "up the middle defense," which basically means catcher, 2b, SS, and CF, is so important that offensive skills at those positions are secondary if the defensive skills are roughly gold glove (or what gold glove should be).
Me, I'm pretty much the opposite. I think "weak bat, good glove" is automatically a utility guy, with the possible exception of catcher. I say that, not so much because Leon and Vazquez ain't hitting much these days, but because Saltamacchia was the polar opposite--good bat, weak glove. He was our starting catcher in the wildly successful 2013 season, and the Sox flat let him go the next year by not making him a qualifying offer.