People saying Theocracies died out and had to secularize...
This is the game where you can reunite the Mongol hordes in to the great Khanate, where you can unite the HRE in to a mega-empire, where you can reform the religion of the Aztec and invade Europe, where you can restore the Caliphate, where you can form Hindustan. You can form the Kingdom of Jerusalem, form a Christian/Protestant empire, save the Ming and alter the history of China, conquer China with Japan, etc.
I don't think having a proper end game goal for theocracies is even the 20th craziest thing that could happen in game. It'd probably be like the 47th craziest thing you could do.
Give theocracies some crazy reform mechanics like the HRE or Aztecs. Make them fueled by religious zeals to pass reforms in to becoming a mega religious empire. Maybe give them CBs on distant enemies that aren't the same religion with the primary goal being to convert their provinces and then the nations themselves. Hell I can see it right now:
Reform 1: Gives CBs on all heretics. During this CB provinces sieged down will be converted, and the wargoal is to capture the capital and enforce religion upon them.
Reform 2: Gives CBs on all heathens, same as the above.
Reform 3: Something something become a permanent center of reformation for your religion.
Reform 4: Something something permanent discipline buff.
Reform 5: Something something kingdom of whatever god(s) you worship. Can now spend excess zeal to build new center of reformations for your religion.
Declaring war on heretics/heathens builds zeal. Taking provinces from heretics/heathens builds zeal. Converting territories/nations builds zeal, converting nations rather than conquering them builds a lot of zeal. Attacking same-religion loses a lot of zeal. Takes X zeal to pass a reform. Changing religion loses all reforms and zeal.
Then just allow any country with completed religious ideas to convert to a Theocracy so long as they have 100 legitimacy and 50 prestige. Add a new government type "dynastic theocracy" and boom you're set.