I see many advantages of using Garmin Lifetime Updater. The most important is that I can have as many GarminDevice.xml files as I want stored directly on the hard drive and download maps for all of the corresponding units. It runs manually or automatically at scheduled times, whatever you prefer in the settings.
With Map Updater you can only connect to one USB or Virtual USB drive and check for map updates. Then you have to swap media (GarminDevice.xml) for the next download. By using Lifetime Updater you can have everything stored in one place and don't have to keep track of device files. I don't use MapUpdater other than for Garmin-Asus or Asian map downloads all other downloads are much easier with Lifetime Updater.