The reason so few people acquire Japanese citizenship is not because of the difficulty doing so, but because it offers little in terms of tangible benefits beyond those already acquired by virtue of having permanent residency status.
1) Citizenship is needed in order to vote. Important for the health of any democracy; but in a country where it seems to be LDP all day every day anyway, immigrants can hardly be faulted much for not placing much value on this aspect.
2) For Americans, Japanese citizenship allows them to revoke their American citizenship, in order to avoid double taxation. (Not an issue for other nationalities, where the ludicrous concept of double taxation doesn't apply.)
That's about it as far as I can think of. Add to that the fact that Japan doesn't recognize dual citizenship, it's no surprise most immigrants are satisfied to just stick with permanent residency.
Note that the bar for permanent residency has been lowered in recent years, making it more easily attainable than an equivalent status in most other industrial nations.