Installation directory choice...
Game files (textures, maps, sounds etc.) are still installed in some folder on system partition while they should be stored in the same location as executables. What's the point of standalone client and choosing installation directory if everything is stored in %AppData%\..\LocalLow\id Software\quakelive\home\baseq3. Seriously
Without writing our own patching service that runs while the game and launcher aren't active (ex. SteamService, HirezPatchService, the PunkBuster services for example) the launcher wouldn't be able to update the game files unless it ran as an administrator. This is not something we're keen on requiring users having to run the game.