Have FIFA stop being so perverse about taking away our rights to exist as independent FAs, or more accurately never start being so perverse about it. Over time a relaxed attitude to national identity (i.e. the lack of a "Blatter will order us to merge!" argument) allows the PL to accept the applications of Celtic and Rangers to join the English league structure. Then UEFA pounces, says that they must rejoin the Scottish system or Scotland will be put under a ban and made to merge into England as the UK. The Old Firm attempt to call their bluff, not believing they will do it, but it goes horribly wrong and UEFA carries out their threat. Banned from international competition and with their primary money-spinner gone, the SFA is forced to merge its competitions into the FA, much to the enmity of both parties. UEFA and FIFA then turn on Wales and N. Ireland, ordering them to do the same despite a lack of provocation. They have no bargaining chips and are forced to comply. FIFA completes the set by preventing the UK from retaining its 4 seats on the IFA, dissolves the IFA and takes full control of international football.
That's essentially all that needs to happen. According to many commentators we're on the brink of it happening anyway, and FIFA are positively salivating at the thought of removing our presence as four separate bodies.
As for the Commonwealth Games, I dunno, just soften attitudes a little and have a vote passed in the 30s or so that the home countries will compete as one, which fails to be repealed following the waves of nationalism closer to the present day.