they tie you up with wikis, bug trackers, pull
requests and a lot of other things around just
git hosting that are difficult to transplant to
another service.
Github has obviously done a great job of making these tools useful and approachable. The point about having ultimate control over that data though is valid. Github might be able to mitigate some of these concerns with something like Google's "Data Liberation Front", providing a contractual agreement with users to make their data easily exportable if they choose to do so. Of course, even that may not be enough for some projects and for them it's a totally valid option to avoid github (and similar closed SaaS options).
The overall issue with SaSS is this. Bit tl;dr, but worth reading it when you have the time:
https://www.gnu.org/philosophy/who-does-that-server-really-s...
In the private discussions I saw, there was some disagreement over whether Github is SaSS or not, but many felt like it was.
(Btw, the official stance is that there is one GNU project with many packages, and all of these packages form part of the GNU operating system. So R, GIMP, Gnome, and Octave are GNU packages and part of the GNU project and operating system.)