Resiliency: Resiliency can be inconsistent with repackaged applications because the repackager utility may not fully understand the component dependencies or what the key paths of the application should be. Therefore, an application may be packaged into one large feature that gets entirely reinstalled if a component keypath is missing. If it were broken up into multiple smaller features it would enable a more manageable resiliency. 

COM/ActiveX Registration: Component Object Model (COM) and ActiveX controls may not be properly registered. Prior to Windows Installer, COM and ActiveX registration was a black box. Except for the exported functions DLLRegisterServer and DLLUnregister server, COM and ActiveX controls offered very few hints of their registration process. RegSvr32.exe was responsible for calling the previously mentioned functions and then the DLL was responsible for registering itself. There is no utility that can view a DLL, an OCX, or an EXE and figure out what goes on inside DllRegisterServer and DllUnregisterServer for that file. There are standard registry entries that most COM and ActiveX controls register, such as HKCR\CLSID, HKCR\ProgID, and HKCR\TypeLib. Information on COM registration may or may not get entered into the appropriate MSI tables by the repackager Shortcuts: Shortcuts may not be created as Windows Installer descriptor shortcuts, which enable resiliency.

Legacy setup shortcuts were .lnk files that pointed to an executable in most cases. Sometimes when the repackager runs, all it knows is that an .lnk file was copied to a directory. For example, a legacy Setup.exe installed a shortcut to C:\Windows\Profiles\User1\Desktop. The repackager would copy the .lnk file directly to the directory listed previously. Therefore, the repackager is not actually copying a Windows Installer shortcut, but rather it is copying a file without any resiliency capabilities included Isolated Components: The only way to take advantage of isolated components is to author a new MSI package. Repackagers currently do not support this feature. Application Removal:When uninstalling a repackaged application, it is possible that the AllUsers profile may be removed. This is dependent on how the legacy setup was captured and definitely needs to be tested.