In my school, probably 90% of professors create their own course web sites (I came across only 2 who use blackboard in 2.5 years). We don't have any problems you mentioned, really, most the web sites are very minimal (even without CSS, usually). It does it's job, everyone's happy. Problem solved :) for example: http://studentnet.cs.manchester.ac.uk/ugt/2013/COMP36111/