Initially, for the first seven years or so, the leagues seemed to match up well against together. That's despite arguments about inherent advantages for AL teams in interleague games (this is part of the reason I don't buy those arguments). But something happened in 2005 or so to push us into an era of American League domination. Payroll explosion? Smart teams in the AL? Whatever the cause, the AL is superior to the NL these days. (here's another look at the same stuff from erosen and stlfan).
The 5-year average (2005-2009) winning percentage for the AL through 2009 is now 0.566, up from 0.558 for 2004-2008.
Let's take a hypothetical 0.500 team from the AL and from the NL from the past five years. The interleague records tell us that the "average" AL team should beat the average NL team to the tune of a 0.566 winning percentage. In order to get the AL team to beat the NL team with a 0.566 winning percentage using the odds ratio and PythagenPat, we have to give the AL team a 26-run bonus to both offense and defense, while simultaneously giving a 26-run penalty to the NL team on offense and defense. That's a 52-run adjustment PER TEAM!
While some have criticized the BtB power rankings' league adjustment for being too large, we only apply a 40-run adjustment per team. Maybe we're being too conservative. :)