Ezra 2

1) The second chapter of Ezra is devoted to a listing of the different family- and city-groups of people who went up from the exile of Bavel to Israel with Zerubavel, Yehoshua, and the rest of the leaders. Verses 3-43 list the groups of the Yisre'eilim, the Kohanim, and the Levi'im who went up. The size of the groups range from 42 (the people of Azmaves, v. 24) up to 3630 (the people of Sena'ah, v. 35), with an average somewhere in the high hundreds (Seder Olam ch. 29 says that the sum is 30,360). From verse 43 until verse 58, it lists the various families of Nesinim and the "servants of Shlomo". Rather than listing each individual family's population, though, the verse just provides a final census count. The total of the 40-someodd families comes to 392. In other words, each individual family listed had an average of 10 members. Why are the Nesinim divided into such small groups? It would ostensibly have been possible to move up by a few generations and combine the Nesinim into larger clans, or to move downwards a few generations within the Yisre'eilim and subdivide them into smaller family groups.
Perhaps when Ezra lists a family group, it means that an entire family group made aliyah as a unit. Although large groupings of Yisre'eilim made aliyah en masse, perhaps no such large groupings of Nesinim made aliyah, but rather just ze'eir sham ze'eir sham. The concept of nesinim making aliyah in itself is a very interesting one, as they were presumably making aliyah with the understanding that they would return to their status as an underclass - whether this is a surprising decision would depend on their status as expatriates in Bavel, but could also be a factor to the fact that the nesin aliyah was made in much smaller groups. It is interesting to note that the number of nesin groups was approximately the same as the number of KL"Y groups - I'm not sure how this impacts the original question.

2) In 2:64, it states the entire population of those who made aliya with Zerubavel to be 42,360. However, when one sums up the all of the families individually, the number is only 30,360, as mentioned above. Seder Olam ch. 29 notes that the families mentioned only represent the tribes of Yehudah and Binyamin (and Levi), while the remaining 12,000 came from other tribes, or 28%. This is a far cry from the impression that I had previously had that virtually the entire identifiable Jewish nation during bayis sheni was from Yehuda, Binyamin, and Levi, with the exception of a small handful (few percent?) from the other tribes that Yirmiyahu had brought back (I don't recall where this is brought down). Ostensibly this proportion might hold until the present day. And wouldn't it be interesting if some of the physical differences between Jews of different regions could be attributed to their originating from different shevatim?