I'm not sure why Adobe makes it so hard to install the flash player with a MSI.  By going to adobe.com and clicking on the "Get Flash Player" link, it will direct you to a page that automatically will attempt to install Flash in IE.  I needed a MSI because I needed to install Flash on a machine with restricted internet access.  Fortunately, even though they don't advertise it, you can get a standalone installer for IE as well...

 http://fpdownload.macromedia.com/get/flashplayer/current/licensing/win/install_flash_player_active_x.msi