Based on what I could piece together, Kuwata surveyed around 300 active pro-baseball players in 2009 on their junior high school and high school baseball years. The questions were broken down into five main categories: practice length, practice methods, coaches, punishments, and injuries.
After sifting through all the responses, Kuwata found that many players questioned the methods that were used on them: excessive practice schedules that led to overwork and injuries; problems with the coaches; finding the right balance between studying and baseball; and whether harsh punishments were necessary. More than half of the players also apparently said that they wouldn't want to coach players using the same methods that were employed on them.
For those wondering, the thesis is 96 pages long.
I'd actually love to get my hands on a copy of his thesis. Sounds like a lot of interesting information. Although I think it would have been even more interesting if Kuwata included questions on current practice methods used by pro baseball teams.
On a side note... I have seen his thesis is labeled as 「『野球道』の再定義による日本野球界のさらなる発展策に関する研究」 but in the program notes, it's listed as 「アマチュア野球の抱える課題に関する研究－現役プロ野球選手に対するアンケートをもとにー」. I'm not really sure which title is correct. They're actually somewhat similar, but the second is more targeted.