Scizor shares characteristics with flying red ants and mantises. It also shares characteristics with wasp-mimicking mantidflies.
According to Bulbapedia, Scizor may be based on red ants and mantises. When going to the Wikipedia pages linked in the Bulbapedia article, the following information can be found:
Fire ant queens, the reproductive females in their colony, also are generally the largest.
The abdomen tends to be slimmer in males than females, but ends in a pair of cerci in both sexes.
Furthermore, Scyther's Bulbapedia page states the following:
Scyther appears to be based on a mantis such as the Japanese giant mantis, with its arms being shaped like scythes.
The Wikipedia page linked in the article for the Japanese giant mantis includes this information:
Males are 68–92 mm in length, and females are 77–105 mm long.
This also explains why female Scyther and, by extension, Scizor, have a longer abdomen than male Scizor and Scyther.
TL;DR: The females of the insects they're based off of are larger than the males.