When Moneyball was published back in 2004, a lot of folks read it and the proverbial light bulb went off. Billy Beane's emphasis on players who did an exemplary job of getting on base seemed so obvious to anyone who had read Bill James's work in the past, but thanks to Beane and Michael Lewis (whose Liar's Poker is even better than Moneyball) there were a million new converts overnight. Beane's salient point was not that on-base percentage was king (even though it is). The most important thing to take away from Moneyball, at least insofar as it would benefit a team without limitless resources, is the constant search for weaknesses in the market.
What Beane found at the time was that a player's ability to reach base with considerable frequency was undervalued, particularly relative to one's ability to hit homeruns. While other general managers were spending top dollar (and high draft picks) for players with pop, Beane narrowed his focus to players with high on-base percentages, who were comparatively inexpensive -- a key for Beane and Oakland's conservative payroll figures -- compared to their homerun-hitting brethren. Even though Beane's shit didn't work in the playoffs, he kept building teams that made their way into the postseason, doing so on the baseball equivalent of a shoestring budget.
With more and more people coming around to the value of walks and getting on base in general, the value of this skill on the open market has started to plateau. I don't think it's overvalued, at least not to the extent that immeasurable traits like grit, hustle and teammate-y-ness are, but I think folks acknowledge the usefuless of these players more so than they did a few years ago. The key, then, is finding new market inefficiencies and the next big undervalued skill (or, perhaps, several smaller-but-still-undervalued skills).
One of those skills might be defense. Defense has always been sought-after, but with newer and better ways of evaluating defensive performance cropping up all the time, a team that can properly articulate the value of one player's defense relative to another's has a distinct advantage. We now know that the players that look the best in the field and who make the fewest errors (and/or have the strongest arms) aren't necessarily the most valuable defensive players. Fielding percentage no longer tells us what we need to know; range-based analysis is where it's at, because more batted balls turned into outs is the most important thing a defender can contribute to the ultimate goal of winning baseball games.
Whatever your opinion of defensive metrics in general, discarding them all out of hand because of their flaws -- perceived or otherwise -- is probably a little short-sighted. Two systems coming to divergent conclusions about a particular fielder in itself shouldn't be grounds for ignoring one or the other or both. On-base percentage and slugging percentage differ wildly about the value of Ryan Braun in 2008, but that doesn't mean we're going to punt them both into the ether. The more data we have the clearer a picture we can draw (of course there is such a thing as bad data, but if you trust the source of play-by-play data then the conclusions of different systems can reasonably be considered in aggregate in an effort to reach a stronger overall conclusion).
Just like offensive value can be expressed via runs created (or some variant thereof), defensive value can be expressed via runs saved, and for all intents and purposes, a run created is as valuable as a run saved. It follows logically that a player who creates 50 runs with his bat (relative to replacement, say) and zero runs with his glove is approximately as valuable as a player who creates 70 runs with his bat and costs his team 20 runs in the field. As a means of player comparison and, perhaps more importantly, player evaluation with respect to acquisitions, you have to consider defensive value in the overall picture. Raul Ibanez might put up decent offensive numbers, but if he costs your team two wins with the glove (not to mention a high draft pick) then you really have to wonder if he's worth the trouble (ed. note: he isn't).