While I had visited once previous, the missus was really hesitant about going to Japan for the first time. I think she was concerned about how expensive it was going to be, how difficult it would be from a culture and language perspective, and it being just a massive urban jungle. But she loved it (as I did my first time) and we've been a back a few times (and hopefully again soon).
IMO, it would help if people understood Japan doesn't have to be expensive and what are ways to visit on a budget and there's quite a bit of English to help get around (and if not, people are really helpful). It also wouldn't hurt promoting some of quainter parts of Japan I suppose.