9to5Mac claims that Helvetica Neue is on its way out as Apple’s system font for OS X and iOS.
Helvetica Neue looks pretty crappy with its custom kerning in OS X, especially on non-Retina screens. (Which a majority of Mac users use and will use for years to come.) I don’t know how San Francisco will look on a non-Retina screen, but it would very likely be no worse.
Personally, I never thought standardizing on one font for all of Apple’s platforms was necessary. But if they’re going to do it, better San Francisco—which was designed for the screen, at least—than Helvetica Neue.