Rudolf was very pro Hungary - the same as Franz Ferdinand was anti Hungarian (though he thought of himself to be anti Hungarian Magnate)
In the end it would nor have mattered -any heuir to the throne would have considered himaelf the emperor of the whole empire and not just parts of it.
What if Sisi and Franz Joesph had another son, born in Hungary? What are the effects on the Austrian succession, on the start of WWI, and his effect on Hungary?
Lets say that he forms an extremely deep attachment to Hungary and adopts Hungarian as his native speech.
I'm thinking more of the aftermath of a potential WWI. Could Hungary ask him to take the throne?