Classes created using Dojo.declared store metadata with their superclasses, so you don't need to use getPrototypeOf.
I think you can get the first superclass with
MyClass.prototype.constructor._meta.bases[1]
and its prototype with
MyClass.prototype.constructor._meta.bases[1].prototype
(the bases [0] seem to be the class itself)
Although why do you need a prototype? Most likely, you will eventually override some function that is already provided by Dojo.declare
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