Warning: I am not a linguist, so my answer is to be taken as an educated guess, no more.
It is essentially historical and the development of this system is told at http://en.wikipedia.org/wiki/Long_and_short_scales . As said above, it is not universal, even in other base-10 languages : East Asia and India have different systems. Even in western scientific tradition, Archimedes used a myriad (10⁴) based system for big numbers and French use the long scale, a 10⁶ based system. The choice of a system grouping the digits by 3 is therefore an historical accident, and we could as well have ended with a different grouping.
However, the need of very large number seems to only exists for some technical use (science, accounting, religion) and do not emerge naturally in the language evolution. Therefore, the systems for big numbers are constructed by the specialist in question and do not blend well with the other numeral. In French, for example, the word "mille" (thousand) is grammatically a number (a cardinal numeral) but "million" is a simple noun. Hence the "need" for a "restart". I guess it's similar for other languages.