(1) Make it possible for a teacher to register and monitor a class. As a teacher if I could find out the activity of my students on this site then I could encourage them by giving extra credits etc. As it is, this is not easy to do. However by making some modifications on the database this should be easy to achieve.
(2) Make customizable LaTeX equation editors. As it stands now, knowing TeX is an entrance requirement. We can get more traffic if we have palettes of TeX buttons appropriate for a particular course.
(3) Add more support for including simple graphics in answers.