There doesn't seem to be a clear mechanism of unit-testing a controller that's used in a directive with bindToController: true. These controllers assume certain properties being set before the execution of the constructor.
I could build a mechanism myself using a temporary constructor etc. but it would be nice to have something in Angular itself.

I discovered the private boolean arg later in the $controller service that serves the purpose:

ctrlFn = $controller(MyCtrl, {
    $scope: scope,
}, true):
ctrlFn.instance.foo = "bar";
ctrl = ctrlFn();

Would you consider making that flag public and thus officially supported?
Or maybe add a helper to angular mock?

See also this Stack Overflow question.