We don’t see much of Jon Arryn, or get to know him personally in GOT/ASOIAF, but he is key to all that happens. It is his death that starts the series off, the conspiracy around his death that turns us all on our heads at the end of ASOS, and the inability of the realm’s Kings to govern without him that drives the entire ‘game of thrones’/political storyline in both show and books.
Jon Arryn was able to unite the Rebellion behind the claim of Robert Baratheon and, given what we know about Robert’s lack of enthusiasm for being king, is the brains behind the period of stability and good governance that marked Robert Baratheon’s reign. But why did the rebellion go so hard, all or nothing to overthrown all the Targaryens, rather than just the unfit for rule Aerys II? Was it just Robert’s personal feelings about Rhaegar Targaryen that led Jon Arryn to lead a Rebellion against the dragon kings, or was there something deeper and more considered going on?
This post is going to lean heavily on the theory of Southron Ambitions, and my own take on it which I term “Southron Ambitions turned up to 11”. The crux of my approach to Southron Ambitions is that not only did the previous generation of Great Lords plan a series of political marriages to unite Westeros more than before following on from buddying up while on the road for the War of the Ninepenny Kings, but there was always an agenda to overthrow the Targaryens. The realm had been dissatisfied with Targaryen madness or unfitness for generations, and House Targaryen now lacked the dragonfire to demand compliance, and was ripe for removal.