At the 140 game point in RT-2, runs were up 15% from MLB. This may statistically be a small sample size for the overall game, but from the posts that have been up & down this BB, it is probably pretty close.
The reasons could have a fair amount to do with the platooning freedom that exists in this game. A team could have a 120AB bench-warmer who happens to slug .750 against lefties in maybe 30AB's against them - enough so he's not considered "platoon" in PB. In real life, you would never PH for, say, Barry Bonds with this guy : In PB, I'd do it in a second if it was late in the game. There are no egos in PB, so you simply follow the statistics.
Platoon may not account for all 15%, but it's a good start.

The simple fact is that this is not real. It's a game, and what says that things MUST be the same. If PB history shows that hitters are 15% more effective than in MLB, than that's what they are - USE that fact and play to it. Draft accordingly, expect to use more pitchers per game, etc.

In my league, Randy Johnson & Pedro are the top 2 pitchers. Sammy Sosa leads the league in HR.
The NUMBERS may not exactly match the MLB, but if you draft, trade for, and respectably manage the better players, you WILL, over a season, have the better team.

If we knew what every player was going to do, we wouldn't need to play - the winner could be determined after the draft.