Using the same retosheet gamelog data as before (2000-2008), I took all of the intraleague and interleague runs scored and allowed data and grouped it by year, home team league and visiting team league.
I then looked at the difference between runs scored and allowed based on whether the opponent was in the same league or not.
First, here are the runs scored and runs allowed differences between facing teams in your league versus the other.
Both numbers are set so that higher is better [RS is how many more runs per game you score in interleague play; RA is how many fewer runs you allow in interleague play].
To put it together, the final chart has the total RS+RA:
The NL stacks up well from 2000 through 2004, but there was a HUGE change in 2005 that has sustained itself over the last four years [and from the 2009 records, I'd guess the gap is still pretty similar].
Perhaps the next thing to look at is what particular thing or things happened between 2004 and 2005 that would have caused a shift like this.