Just tried out the new patch - I like it a lot so far! Cities definitely seem to grow more slowly early on, but can blossom once you gain access to a variety of resources. Some notes:
The new jeweler and tannery buildings require an improved resource in their vicinity to function, but only need that resource in your empire to be built. Cities that shouldn't be able to build one will have it show up in their building list, but if you build it, it will immediately deconstruct. These should probably be changed to needing the resource in their vicinity to be built in the first place.
Barbarian forts no longer spawn when generating a map with the PAE map scripts, though this may be intentional. Barbarians and animals seem to slow the game a lot less, which is good.
And Tia's right about the orthodox church - The 4th Ecumenical Council is when Chalcedonian Christianity (what we'd know as Catholic and Orthodox today) and non-Chalcedonian Christianity (namely the churches of Alexandria and Armenia) split. Catholicism and Orthodoxy had regional differences at this time (mostly over the supposed primacy of the pope in Rome), but wouldn't really start to grow apart from one another until the 800s, and wouldn't formally split until 1054, which is probably outside of the timeframe of the mod. I'm not really sure what a good way of representing the Ecumenical Councils in-game would be... Creating a religion for every major Christian branch seems like it would be a bit superfluous (though if you did, I'd say Arian at the first council, Nestorian at the third, and Miaphysite at the fourth), but maybe there's a good way to represent the various creeds being confirmed as orthodox or heretical.