I'm not a big soccerfan, but I know 3 things:

Best player in Japan? Keisuke Honda

Best Japanese Player playing abroad? Keisuke Honda

Favourite all-time Japanese player? Keisuke Honda

:p

Oh, and I like this team: Japan national football team - Wikipedia, the free encyclopedia

Favourite Japanese club? Dont have one. I like all the J.League, but not too keen on Kashima Antlers
Best player in Japan? Genki Haraguchi
Best Japanese Player playing abroad? Shinji Okazaki
Favourite all-time Japanese player? Shunsuke Nakamura
Favourite year for the Japanese National team? This year...Asian Cup & Womens world cup final
and finally.. Any recomendations to improve the quality of soccer in soccer in general? No need. The Japanese soccer scene is on the up

Favourite Japanese club?
Nagoya Grampus

Best player in Japan?
Hiroki Sakai

Best Japanese Player playing abroad?
Yuto Nagatomo

Favourite all-time Japanese player?
Yuto Nagatomo
Favourite year for the Japanese National team?
2011 :)

Favourite Japanese club? Shimizu S-Pulse

Best player in Japan? Nakamura

Best Japanese Player playing abroad? Honda

Favourite all-time Japanese player? Akira Kaji

Favourite year for the Japanese National team? 2002

and finally...

Any recomendations to improve the quality of soccer in soccer in general?
Improve on defense. Very good mid and front lines. but need a bit more in the back.

Best Footballer.....
 

Former Celtic star Shunsuke Nakamura has criticised his fellow countrymen as insular for staying at home and urged them to play abroad for their own good and to boost Japan’s place in world football.

But....
I would say in their best days, Nakata was far superior to nakamura.

Although nakamura got mvp in the Scottish league, it is only the scottish league (no offense to scottish people). This year was their first time to get past group stages in Champions League., and even minor leagues like Dutch league has produced number of Champions League winners. J-League is probably similar to the SPL in quality.

But Nakata on the other hand has received awards as best international player in Serie A, one of the best leagues in the world. My vote goes to Nakata.

Its also worth mentioning Okudeara, who was a defender for FC Koln in the 70s. He was supposedly a ver solid defender.

Is there soccer clubs in japanese schools?