Pujols' selectivity definitely makes it more likely that he will be a better hitter going forward, mostly because the K rate. Also, Pujols makes contact when he swings far more often. While they swing at the same percent of pitches outside the zone this year, Pujols makes contact on 78% of them while Votto hits 68%. Votto has twice as many swinging strikes as Pujols.
However, Votto has done about as much as Pujols this year with the at bats he has. Pujols has also grounded into 11 more double plays than Votto- not only unproductive outs, but producing an extra out.
I guess the point is: Pujols is still a better hitter, but Votto has had just as productive a year (their production is actually amazingly similar). While Pujols' superior contact rate will likely help him produce more than Votto in the future, I think MVP should be more about production this year.
It will be interesting to see how things change moving forward to the end of the season, but these two guys are neck and neck, in my opinion.
On a sidenote: I love fangraphs. The amount of data there is amazing.