I had assumed apostle was just the new name for the missionary unit, but now it seems like there are both. I wonder what the difference is.
What I suspect is -
Great Prophets are now earned from Great Prophet Points.. So faith is no longer necessary to get Great Prophets.
Here is where the speculation begins - I'm assuming that Great Prophets no longer convert cities - they are probably limited to founding/enhancing religions and maybe holy sites? They say that Great People will draw from a pool but I highly doubt the devs will create specific Great Prophets based on real people - I think it is a subject that is too sensitive.
Apostles & Missionaries presumably cost faith to buy. So now it should be easier to spread a religion as you don't have to choose between spending faith on enhancing a religion or on missionaries.
Apostles are possibly more expensive and may convert citizens of an existing religion - much like the Great Prophet does (think of the 12 apostles of Jesus converting the Jews and Pagan religions to christianity)
Missionaries might be cheaper and used to convert citizens with no religious belief?