C2 will probably never export swf, but I could be wrong
C2 currently exports in HTML5, a platform that is becoming more and more important, and soon will be as popular as flash. I believe all these websites will be accepting HTML5 games sooner or latter (I know Krongregate does already)
CC is better to make windows games, and bigger projects. Its more advanced than C2, but has a lot of bugs (CC might crash easily, so you should save your project often)