It was Vaganova's method based on her own experience as a teacher and modified when the technical demands of the company needed it to be. (Up to a point: according to Catherine Pawlick's book, "Vaganova Today," at a certain point she did think it was crossing the line into gymnastics.)
Anytime something is codified, it already has a point of view, whether by fiat or committee, and, by definition,different things are diminished or lost, while others are emphasized more strongly. There wasn't just one path from the Imperial School: Vaganova developed one that is the basis for many schools and has supported a major company with continuity over the decades and many other companies as well throughout Eastern Europe and former Soviet Union, as well as a few Western offshoots.
Vaganova wasn't the only one, but she's one whose teachings have been institutionalized, have had continuity across generations, and haven't dissipated in the same way that many other great teachers' have.