All variable and class types in ActionScript 3 are child classes of Object, so in terms of functionality, I don't think there is any difference between the two.
Some sub-classes of Object like int and Number behave like stack objects (this means that var firstInt:int = 5 and var secondInt:int = 5 actually point to the same Object), but that doesn't affect how they are treated when you point to them using a generic variable.
If I could hazard a guess, I'd say they added the wildcard as both a way to save typing and to make it easier for C/C++ migrants who are used to referencing generic types with a void* pointer rather than a base Object type.