Actually, I don't think your results indicate what you think they do -- they seem to be as expected if the players were treated fairly. You have a lot of noise in your analysis, especially including R and RBI. But even working with that, Olerud would be favored in your work by about the amount he was.

Consider:

1) The player's real stats are adjusted by the park they played in. (At least I've always understood them to be.) Mike has never explained exactly how it works, but I'd assume that Olerud's average gets adjusted up by 3%, half of Safeco's Park penalty. All his XBHs are increased upward to nuetral-park level. Pujols would be adjusted only slightly.

Next time, compare Helton to Sean Green. I'd bet Green comes out far better.

2) Platooning. Olerud is a far better candidate to platoon than is Pujols. He had more than 25% of his MLB PAs vs LHPs; I'd guess that in some PB leagues it's much much less than that. Look at how much difference that would make!