For defense and position, I used the position the player played the most in 2012 and obviously only compared positions when using range factor (the official NPB site splits the positions nicely). I couldn't find a positional scarcity model that I liked (and was easy to use for these purposes), so I used an extremely lazy one. I used Baseball Reference's 2012 MLB batting splits and sorted the positions by OPS. It is the MLB obviously, but I think the general rule applies across baseball. 1st Base is the least valuable position (6 in rankings), while shortstop is the most valuable (1st in rankings). I used these rankings to go into the total rankings (and of course averaged out in the average ranking). I didn't know what to do with catchers' defense, especially since the NPB didn't keep track of CS% data for the Ni-Gun, so I just used Range Factor. I couldn't differentiate between CF and corner outfield, so I didn't when it came to positional value (outfield ranks right behind 1B in our crude positional scarcity formula), but it should separate correctly when looking at range factor.
So overall, this is really crude, especially since it weights OPS + more than anything else and there are major defensive component problems, especially with outfielders (who get penalized in the rankings because there are so many of them). I don't trust it as much as the pitcher rankings, but here it is nonetheless: https://docs.google.com/file/d/0B_DUd_c_mKWrWWY3TjlBSGZpR1U/edit
The Top 5 Position Player Prospects:
1. Tetsuro Nishida
It seems that what the Golden Eagles lack in pitching prospects, they make up for in hitting prospects. Nishida is the older of the two shortstops, but he also played much better defensively and hit slightly better in 2012. He shows good bat control and an approach that seems to use the whole field. I like his size and his swing is good as well.
1. Daisuke Nakai
For a 2nd baseman, Nakai has a really big looking frame. This didn't stop him from getting to a lot of balls defensively. At the plate, he also doesn't look like a 2nd baseman either, with a large uppercut swing. It looks there is power there, but one wonders about the approach.
3. Takumi Miyoshi
If defensive data is any indication, Miyoshi should probably not be a shortstop. However, with Nishida most likely ready to make NPB impact before Nishida, this isn't a big deal. He looks smaller than Nishida, so you wonder where the power is going to come from in the future, and he seems like a ground-ball hitter, but having Miyoshi is good insurance for the Eagles.
4. Itaru Hashimoto
Despite his good hitting statistics, Hashimoto appears to be a slash and dash type player. As the only outfielder on the top 5, he probably needs to be a centerfielder to have premium value, but he had a good range factor, suggesting he is good defensively and may stick there.
4. Tu-Hsuan Lee
A corner player, he is a rare right-hander with an open stance. The body screams 1st basemen, and the defensive data suggests that he doesn't have great range at 3rd base. This just means he will really have to hit, and there may be a few causes for concern. He walked just under 10% of the time, and struck out 18.2 %, not bad, but not really excellent. He definitely comes with some risks, especially considering his swing mechanics, but power can be hard to find in Japan at times, and Lee seems to have some of that.