Using something other than the officially supported system creates friction for the students, who generally are not as computer savvy as one might expect. We use Blackboard at my school, and it links into the the time schedule and grading. So the default course page students see is the one on Blackboard (mine redirects to my regular department page), and you can't officially post grades other than on Blackboard. I also have to go into Blackboard to see who's still registered (although this information is out of sync with whatever the official system is).