The VideoLAN Forums

Here is how to do a silent install of 2.2.1
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Instructions
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Install VNC
Launch
Disable privacy settings
Set fullscreen
Set any other required settings
Close VLC
Copy the 2 vlc* files from %appdata%\vlc into .\DefaultSettings

Run Install.bat to install
Run UnInstall.bat to remove
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Create an install directory with the following...

DefaultSettings - Directory that contains vlc-qt-interface.ini and vlcrc (Captured from earlier)

Install.bat
@echo off
.\vlc-2.2.1-win32.exe /S
if NOT exist "%programdata%\vlc" MD "%programdata%\vlc"
xcopy .\UserSetup.bat "%programdata%\vlc" /I /Y
xcopy .\DefaultSettings\*.* "%programdata%\vlc\DefaultSettings" /I /Y
reg add "HKLM\SOFTWARE\Wow6432Node\Microsoft\Active Setup\Installed Components\VLC_2.2.1" /v StubPath /t REG_SZ /d "c:\windows\syswow64\cmd.exe /c %programdata%\vlc\UserSetup.bat" /f
reg add "HKLM\SOFTWARE\Wow6432Node\Microsoft\Active Setup\Installed Components\VLC_2.2.1" /v Version /t REG_SZ /d "2.2.1" /f
del "%public%\desktop\VLC media player.lnk" /Q
exit

UnInstall.bat
@echo off
"%programfiles(x86)%\VideoLAN\VLC\uninstall.exe" /S
timeout 5 > nul
rd "%programdata%\vlc" /S /Q
reg delete "HKLM\SOFTWARE\Wow6432Node\Microsoft\Active Setup\Installed Components\VLC_2.2.1" /f
rd "%programfiles(x86)%\VideoLAN" /S /Q
exit


UserSetup.bat
@echo off
if NOT exist "%appdata%\vlc" md "%appdata%\vlc"
xcopy "%programdata%\vlc\DefaultSettings\*.*" "%appdata%\vlc" /I /Y
exit

vlc-2.2.1-win32.exe - Downloaded .exe

But I assume this will install Web plugins and add Context Menus, right?
I seem your solution install VLC with defaults properties and THEN you change Preferences afterwards.