I'm reading in the newspaper that a large majority of the home runs are off of sliders that hang out over the middle of the plate. Matsuzaka's success the past couple of years with the slider has probably prompted other pitchers to try it, and they just haven't mastered it yet.
Also, for some time now, I've been thinking that the larger stadiums have gotten batters to improve their power to continue being home run threats. Back in high school, I always played tennis better when the opponent was above my level. The larget stadiums may be having a similar effect on batters. After all, when Tokyo Dome opened in 1989 (I think?), all the "experts" proclaimed that it was the end of the long ball era. Yet Mitchell hit a ball over the billboards in left field last night for a monster home run. (He hit the ball too far for a new car.)
And that brings me to another hypothisis. It seems to me that the balls carry better in the domed stadiums. I doubt that it's air conditioning blowing the balls toward the stands. The air pressure tends to be higher (especially in Tokyo Dome) to help hold the roof up - which is the opposite of Colorado's thin-air long balls. So is the lack of wind a factor? I don't know.
As you said, this opens up a lot more doors, raising more questions than answers.
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This is probably more of an opinion question than a simple answer question. I've noticed that the Pacific League is cranking out far more home runs (even after taking the fact that they started a little earlier) yet the Central League has all the littler stadiums, such as Hiroshima, Jingu, and Yokohama. In the Central League, the Tokyo Dome seems like an average place, but in the Pacific league, compared to all the deep major league size power alleys of every other stadium (Seibu Dome excluded), balls seem to launch out during Fighters games.
This is probably a question that opens a lot of doors because I remember Jim Allen's guide dealt quite a lot with this. I'm just wondering is Nakamura's 39 home runs is a greater feat than Matsui's 42 because of the smaller stadiums and friendly power alleys of the Tokyo Dome, or is it that players have adjusted to the stadiums and have built up their power in order to clear the fences?