Part of Ottoman administration was the millet system, a non-territorial jurisdiction designed to oversee the various religious groups so they would be tried by their own laws, look out for their interests etc.
Eastern Orthodoxy, Armenian Copticism, Judaism and of course Islam all had a millet overseen by a paramount leader installed in Constantinople. Catholics due to their small numbers never got a full blown millet and Sulieman the Magnificent gave the honour of protecting them to Francis I as a gift. This gave France a solid excuse to intervene in the Empire in the 19th century but that's another story.
Anyway may question was, what if the Ottomans conquered more territory including even more diverse religions, how do you think new millets would be organised?
Now like the Catholics OTL, various Protestant sects that flourished in occupied Hungary were simply given protection by the puppet kings of Zapolya however I'd be interested in possible 'paramount leaders' in particular.
As well the west, how do you think Indian religions like Hinduism, Buddhism, Sikhism etc. would be dealt with if the Ottomans had commited more to the Indian Ocean and got a foothold on the sub-continent?