About your application: how technical were the questions in the interview? And how long was your project proposal?
I know you aimed this question to madphysicist, but if I may add, in my local consulate web page it was suggested that the proposal should be limited to 15 pages. I guess the idea is to show them that you have a worthy thesis without giving them tons of reading in order to reach such conclusion.
As to the interview, I was lucky that of the interviewers was a lawyer of exactly the same research area that I am (Intellectual Property), so I could deepen my explanation a little (which helped me in the overall score, as I've been told). The other interviewers, however, weren't lawyers, so they basically focused on whether or not I would be able to adjust to Japan (
i.e., culture shock, family issues), if I had the interest of learning the language and customs, what was my purpose there, what I intended to obtain with my research, etc.
One tip I've been told and that certainly helped me is: go presentable. If you're a male, suit up. If you're a female, dress formally as well, and don't show any cleavage at any costs. Most people that were competing with me went there with jeans and t shirts, which I found out later not to be the best outfit for an interview with Japanese people.