Seriously, do it player by player.
You play aus v eng - link player by layer in those teams and at the same time youre also populating eng,aus domestic and IPL with a single instance of the player that you have chosen.
Then you want to play sa v ind - you do the same, again another whack of domestic players populated by a single instance of the player you have chosen.
Only if you're launching straight into a eng county championship mode will you have an unmanageable amount of linking to do. But actually because you have CA beta in advance you don't have to do it in one big whack.
Get best, or a theoretic get all don't work. Even if Big Ant implemented a solution where get best on a team got you the best rated instance of each player in the roster, which would mean you did keep a single Cook etc. across the game, you're still dealing with the vagaries of rating.
Player by player as you need to play with them, that's the only way.
And always remember not to add the downloaded to a team. Leave him in free agents, do the link, then delete him.
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If you want to do a career mode straight away, then do each international team as i suggested, then do the country you want to play in team by team (you'll find lots of players linked already through the international linking you did... Plus IPL if you want to play that in your career...
It's easy enough for big ant to implement keeping a single instance of the player, as i pointed above get best would mean not the best rated team just the best rated instance of each player on the roster, taking account of already linked players and maybe giving you an option to switch or keep...
But how to create an algorithm that ignores the terrible rating consistency of moronic Joe Public, that i don't even want to try and think through.