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While I understand the urge to ignore the R and RBI categories, Matt ... there is something that they capture beyond physical ability.  They capture BOTH playing time and deployment choices of previous managers.  We all understand that lineup placement is more critical for RBI and Run totals than simple ability.  Leadoff hitters score runs and don't get RBI -- 3/4/5 guys get RBI.
But, for good or ill, the vast majority of baseball choices are very, very similar.  The managers are an inbred species, who often make choices based far more on what they are looking at then what the numbers tell them.  If you get a 6'4" 230 pounder with speed, you simply won't see him leading off in most cases.  So, I could see R and RBI being indicators that capture PT and deployment likelihood, (which, of course, impacts production).
Ultimately, however, I think it is simply a case of understanding that you're going to appeal to a much wider audience if you include the most familiar stats in the mix.  There are many, many players that still insist on the value of R and RBI ... and will dismiss any system that opts to ignore them.  Even today, the vast majority of ROTO leagues are based on which stats?  R, RBI, HR, SB.  It's a big leap from F = MA to E = MC^2 --- non-scientists need time to catch up.  And James has always been a leader in the industry NOT because he's the best scientist, (he often notes this himself), but because he is a master of communicating the science to the masses.  Opting to include the classic stats is a part of that communication.