When flash banner first came onto the scene I didnt pick up on them because statistics showed that a good percentage of my sites visitors were still using older browsers which may or may not have had flash capabilities. Today Id hope that a very high percentage of everones vistitors do have flash enabled browsers that do not require additional downloads.
With that said the only thing that Id see serving as a deterent would be quality as the professor has detailed. Create something that says click me and all your affiliates will be using it! Visual impressions / presentations are everything in a banner and if its simply ugly it simply wont get any clicks.