I believe the proper way to do it would be to evaluate each player's defensive value on a scale where the average shortstop will rate higher than the average player at catcher, and so on down the defensive spectrem.  However, often fielding methods are done in terms of runs above some baseline, with the average player at each positon being a 0, which necessitates some kind of positional adjustment. 

 

The easiest way to do this is to look at the offense at each position, and to force the baseline player at each position to be a 0 offensively.  However, the fact that the current crop of shortstops are better hitters than some from the past should not make shortstops as a whole less valuable, because their defensive value remains unchanged.  However, the logistics of a defensive positional adjustment are difficult to work out.

 

This chart gives the offensive positional adjustment based on Runs Created/Out for each position in each decade.  The PADJ is just Pos RC/O divided by Lg RC/O.  The Lahman database was used for the data-each player is classified at a postion based on the position at which they played the most games in each season.  There is no LF/CF/RF breakdown for outfielders, which would be very helpful, because that information is not in the Lahman db.  Anyway, you can draw your own conclusions from the chart.