The KyngChaos method is the one-stop shop for Mac users to install QGIS. This page has links to the critical frameworks and python modules, which he graciously packages and maintains himself. Have people have had success selectively installing some of those components but not others? Or replacing them with updates? Which packages are mission critical, and which ones can be replaced or updated?
I have had installed the KyngChaos versions of numpy (v. 1.9.2), scipy (0.16.0), and matplotlib (v. 1.4.3). I have uninstalled these versions of numpy and scipy, removed the
.pth overrides in order to update via
sudo pip install -U, and have had no adverse effects (yet). But QGIS does not like it if you do the same with matplotlib.