I knew someone was going to mention the II's.
They are most certainly an exception to the rule. Not only were they the least desirable Mustang built at the worst point in automotive history, but their production numbers paled in comparison to the much more popular '87-'93 EFI Fox bodies.
I think desire for the car istself plays the biggest roll. I wouldn't say "wildly popular". Nobody wanted the II's when they were brand new, as they were always known as a piece of @*%& red headed step child of the breed. But, if you wanted to drive a Mustang between '74-'78, the Mustang II was your only choice. The Fox was considerably less @*%&ier and thus more popular and the newer stangs got progressively better still.
Not to mention...where's the aftermarket suport for the Mustang II? Almost nothing. Every Mustang built afterwards though has a huuuuuge aftermarket backing, which is one of the major things that continues to make these cars so popular IMO.