There are two probable reasons for Gene selecting WWII as the "moment in history against which he measures all else".
First, this war was an incredibly important event in the 20th century - probably the single most important "event" of the modern era. WWII effectively determined the shape of the world economy from 1945 to the present while also essentially ending the practice of colonialism-by-occupation. Women were brought into the work force in the U.S.A. and in England as a result of war needs. Nuclear power became possible due to war research. Capitalism became the dominant national-economic mode globally. For these reasons and others WWII was an event of huge impact and proportions.
Second, this novel is a coming-of-age story. Gene is involved in a process of exploring and establishing his identity. The reader follows Gene and his friends from the last definitive days of childhood (playing games during the summer session before becoming a high school senior) to the brink of adult life (when Finny dies and Gene realizes that he must accept his guilt over Finny's injury and death and move into the world bearing that burden). Until they went to war, the boys at Devon would be just that - boys.
They were carefree, and the older men (all too knowledgeable about the straining effects of war) admired these students’ situation: Gene, Finny, Brinker, and the others were all young men on the brink of going off to war but still inhabited a pocket of time in which they could live joyfully. (eNotes/Masterplots)
The war represents, symbolically, "the world" at large and stands as the ultimate test of character. Thus it is the natural backdrop for Gene's story wherein his character is repeatedly tested and where he finally realizes that he will have to make his own "separate peace" with himself.
To make this into an analogy: as WWII changed the world, so is Gene also changed by his last year at Devon.