I just gone through a useful link by Serge in which he states 6 points you should follow while developing a RIA which wont annoy the end user as well as make sure they wont uninstall your application if you take care of some small stuffs while devloping it.
Your RIA should be compatible to all the below scenarios and less annoying.
1 Launching your application on login/startup-(Ask user preference after installation or add a checkbox to preference tab)
2 Always in front-(Ask user preference)
3 Automatically setting the file type-(Ask user preference)
4 Full screen applications(Should be based on the necessity and in full screen mode add buttons or shortcuts to jump to other applications)
5 Custom chrome- Minimize and close button is a must
6 Self signed applications- Get signed certificates for commercial application everybody is scared of harmful application.
Click the following URL for more details.
Best practices for RIA