Remember how I strongly I disagreed with picking Justin Morneau over MVP for AL MVP? Well I still do and here's another reason why:
As I mentioned before, shortstop is an inherently more valuable position on the baseball diamond than first base. Very few players can play shortstop effectively, while almost any major leaguer (and many minor leaguers) can be an average first baseman. So if two players, A and B, had the exact same numbers over the course of a season, while A was a 1B and B a SS, B is more valuable.
How much more valuable though? I think the best way to look at it is as so: When A produces his numbers at 1B, he relegates the team to playing an average SS. But when B plays as well offensively as A, he allows the team to pick up an average 1B. So the difference in value between A and B is the difference between an average 1B and an average SS.
Luckily we can figure that out statistically. Here's a list of the positional averages in both leagues this year. One of the comments has a link to an excel spreadsheet that breaks down the averages in each league. 1B have an average OPS of .819, while SS (not surprisingly the worst offensive position in the league) have an average OPS of .742, a difference of 77 points.
Last year Jeter's OPS was .900, while Morneau's was .934. If we add the difference in OPS between positions to Jeter's OPS, Jeter's OPS ends up being 33 points higher. (As an aside: Jeter's OPS+, which takes into account ballpark factors is 138 or 38% over average, while Morneau's is 140, only 2% higher than Jeter’s. These numbers do not take into account positional differences.)
Even more striking is Jeter's advantage in OBP, which is overwhelmingly considered the more important part of OPS by most sabermetricians (in Moneyball it noted that Billy Beane considered a point of OBP to be three times more valuable than SLG!). 1B average a OBP twenty points higher than SS. If we add twenty points to Jeter's .417 OBP, we get a .437 OBP relative to Morneau's .375, a 62 point differential. If each point is worth 3 times as much as a point of SLG, then Morneau's 21 point SLG advantage after adjustments for position (Morneau hit .559, while Jeter hit .483. But since 1B have a 55 point advantage in slugging over SS, Jeter's SLG relative to Morneau was .538) is greatly outweighed by Jeter's overwhelming 62 point advantage in OBP.
Put simply, there is no serious statistical analysis that finds Morneau more valuable than Jeter.