Well, why did the missions fail? I know virtually nothing for the history of the RCC in Japan, so I briefly looked it up on wiki (I know, not the best source in the world, but it's not even my church) and saw that the initial contact in the 1500s was marred by misunderstandings (the Japanese apparently thought Christianity came from India) and suspicion (since converts were encouraged to adopt Western names and culture). I'm assuming that the situation is different nowadays, but fixing very basic things like that is a good idea if you're going to try to witness to any people. Most people in the world have heard of Christianity, but maybe have a similar set of presuppositions about what it means to be a Christian such that it becomes distasteful or a non-option for them. Most of the places where Christian mission has failed are those kinds of places: the missionaries came with a foreign culture to upend or replace the native one (it should be obvious why this doesn't work, right?), and/or were not responsive to native concerns, questions, or values. There is probably also a limit to what you can do to baptize the culture, anyway, as certain things (like the religious syncretism mentioned by LoAmmi) are probably not what you'd want to encourage in the name of gaining converts, but to the extent that you can, it is good to make the burden easy. Many cultures have analogues to preexisting Christian practices or beliefs, so doing your homework goes a long way.
I don't think God ever wants Christianity to fail anywhere. I think some of the people representing it kind of set themselves up for that, though. When I was a child I went to Mexico with my mother's (Presbyterian) church group which was intent on witnessing to the people there...despite the fact that I was the only one who spoke Spanish or knew anything about the culture, and I was decidedly not intent on that (my dad's side of the family is all Mexican and Irish Catholics, so I never had the idea that Catholics needed to be converted to Christianity in the first place). The "training" video they had us watch before going was seriously mostly about how it's not okay or funny to answer the border guard's questions in Spanish or make jokes to them about how you're smuggling illegal immigrants. So it's not surprise that when we went there the missionary aspect of the trip (as distinct from the building houses and setting up a health clinic aspect) was a total failure, since the majority of the people could not communicate with the locals, and the older kids (teenagers/early 20s; I was 12) mostly treated it like Spring Break vacation and were loud, obnoxious, and laughing at all the funny "stuff" they found in Mexico (how stupid does your whole team look when half of it is laughing about a brand of bread sold there called "Bimbo", and gathering to take pictures under advertisements for it? The Mexicans probably thought we had taken some mentally-defective people with us, for some reason).
From my own experiences, there are many more ways for a mission to fail then there are for it to succeed, so I think other people who have said that 1% is not failure are probably at least somewhat right.