That's my preference as well, but integrating it with your app launcher of choice (among other things) can be a little more challenging. The alias in /Applications is a particular pain if you try to use Alfred or Spotlight, but maybe Quicksilver works fine. You only need to open emacs on startup anyway. :-)
I just mv the .app from the Cellar to /Applications so that spotlight can find it.
brew upgrade misses out then. I add Cellar/emacs to Alfred's search path and brew upgrade/cleanup more or less works fine.