Leagues with low MLEs (even if your ML is set on default, the minor leagues all have progressively lower MLEs) have low ERAs. It seems like this is due to the Batting Average MLE having a more obvious affect on hitters than pitchers, as pitchers don't have a rating that corresponds to Contact for hitters.
I've also heard others say that their 6.x leagues imported with low ERAs initially and as time passed the ERA increases. This is probably due to an interaction between the League Totals that are based on the imported players and the ratings relative to each other and the new talent created by the new PCMs. If there's an imbalance between the ratios of ratings of the imported players vs the created ones that enter the league you'll see a change as the league becomes more and more slanted towards the players created in OOTP06.
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