The system used for small numbers is probably a broad extension of an earlier dual number for nouns, i.e. something like a plural but just for two things. For (some) male nouns, the nominative dual ending was the same as the genitive singular, which was then extended to all other nouns even when this correspondence didn't hold, and from just 2 things to 3 and 4 as well. Nowadays the dual has been completely forgotten for nouns, and the only interpretation of the rule is that it's a genitive singular.
Russian distinguishes paucal (few) from plural (many). It’s not super common but there are some other languages that do it.