One reason--there were never enough missionaries.
Here is a quotation from Diego Pacheco. Xavier and Tanegashima. Monumenta Nipponica, Vol. 29, No. 4 (Winter, 1974), pp. 477–480 on the Japanese mission.
In Cangoxima, the first place Father Master Francisco stopped at, there were a good number of Christians, although there was no one there to teach them; the shortage of laborers prevented the whole kingdom from becoming Christian.
And, for a good read on the miracles of this talented saint, read this, by John Hardon, to whom I pray daily to heal my asthma. http://www.therealpresence.org/archives/Miracles/Miracles_005.htm