Just my speculation...
Well, SFO has been in operation in one form or another since 1927, so it long predates wide-body jets - or even jets, for that matter! It has operated parallel runways since at least Word War II, so the "designers" just could not have known that the runways would be too close together. Other strategic international hub cities have built new airports that are better equipped to handle intercontinental aviation, but that has never happened for San Francisco. OAK and SJC have never been elevated to international hub status, and the environmental impact of expanding SFO via reclamation of land in the bay would make it politically impossible.