If you delete the plugins and cache (Located: C:\Documents and settings\User (you)\Application Data (folder is hidden; make it visible)\vlc) then this may resolve the problem.
As for skins it can be a little tricky. The first way you can try is through the player. Go to: Preferences > (tab) Interface > Main interfaces. Set the Interface module to "Skinnable interface", save and restart VLC.
If that doesn't work for some reason then try this through the start menu: Start > All Programs > VideoLAN > Quick Settings > Interface > Set main interface to skinnable.
Now the rest is simple. Download a skin from the
Skins page, unzip the file, go to the directory where you installed VLC and put it in the "Skins" folder. When you want to change a skin just right-click on the interface and "select skin".
This whole process will become easier in the next version of VLC.