The choice of the 'right' fonts is very situation-dependent. A font
that's perfect for body copy might be terrible for headlines, and vice
versa. Therefore, the selection of typefaces can not be left to the
operating system, because as you rightly pointed out, it will always use
the same default font. While that default font probably isn't the worst
of all fonts for any situation, it is certainly not the best.
However, delivering the best experience must be our goal. Therefore, it
is important that the decisions which font to use in which situation is
consciously made. Using a font stack is just a good practice to ensure
that users who can't load webfonts or whatever still get a font that was
picked carefully to suit the situation. That way, we as designers can
still deliver the best possible experience even to users who for
whatever reason can't use our first font choice.
best, max
@awesomephant