Difficulty in application updates
In Microsoft windows installer deployment strategy the entire application needs to be reinstall whenever an application is updated while in the case of click once deployments strategy application updates are provided automatically. Firstly only the modified portion of the application is downloaded, and then the entire application is downloaded. Lastly only the update application is reinstalled from a new side by side folder
Impact to users computer
Application are resides on shared location so that resulting in version conflicts such as more than one assembly have a same version number while in the case of click once deployment each application is self contained and does not interfere with other applications.
Windows installer methodology requires administrative permission for installation and un installation strategy while Click Once deployment does not needs administrative rights for installation and un installation process except only code access security.