Of course you can always madmod the modmod to suit your own tastes, and you should if that's what it takes to have fun.
I've done a few tweaks myself, mostly just to test out some of the ideas I've tossed out in this thread.
I do think there are a couple of things to keep in mind about changes to this mod, especially if you are advising the creator on what he ought to do.
Playability: It's not supposed to be
easy. Putting temples in all Byzantine cities renders the Cathedral UHV absurd. Leave aside the lack of challenge in building two Cathedrals by a late date. Since you start with the ability to build two Cathedrals, you no longer have the "interesting choices" in how to balance missionary/temple building with your other needs (including seeing off the Arabs), or in deciding what civics would give you Cathedrals most quickly and painlessly.
If the core cities start that large and powerful it also unbalances the tech race. Constantinopolis gushes lightbulbs/coin when it gets big, and it gets big very quickly even without worked seafood tiles. It gets so big so fast that I generally have to turn off growth before I've even built workboats.
Add Philosophy to their tech lead? Researching Philosophy is part of one of their UHV conditions.
Basically, if you make these changes to the Byzantines, you
must come up with at least two new UHV conditions to replace Cathedrals and the Tech race.
Historical Accuracy: I like historical accuracy, and I've proposed adding Meditation and a few Monasteries, so I dig what you're saying. But I also think historical accuracy needs to take a back seat when it undercuts the challenge of play. Besides, if you want to be historically accurate, the mod should cede the Arabs Egypt, Africa, and Hierousalem at the start, and you should play your part by trading Alexandretta back and forth with them.
Besides, I'm not sure that the set up is that unfaithful to the Byzantine Empire c. 600. The empire had just emerged from the local equivalent of a "world war" against the Persians and was in an exhausted and debilitated state. (One reason the empire was such easy prey for the Arabs) They barely managed to hold them off, and then went into a decades-long process of rebuilding and strengthening themselves. This is the process you are asked to recreate. It makes sense that you start with a shambles.
That is something very important to remember about RFC, I think. In RFC you are not given a civilization that looks like the real-world analogue. You are given a set of materials and basically challenged to replicate the real world analogue, and improve upon it. If you wanted Egypt in the 3000 start to look like the real world, you'd start by giving them two cities, the Pyramids, Great Lighthouse, Great Library, and 5000 culture points. But no, you are told that you have to
create these. It's the same with the Byzantines.
Specific reactions to specific changes you've described:
1. Add City Dyrrachium (NW of Athenai), 1 Longbowman, harbor: This is something easily done in-game.
2. Christianity spreaded to ALL Byzantine cities (or its heresy!!! the byzantines are pretty nasty fellows.): This is a UHV requirement. Why start with it?
3. Add aqueduct to capital (Constantinople had a awfully huge one): Easily added in-game.
4. Add christian temple to all cities (Byzantium is VERY religious): Another UHV goal.
5. Add five triremes and a galley to capital (wheres the byzantine navy?!): Easily added in-game. In fact, in a typical game, by the time I get Astronomy, I have one of the largest fleets in the world, and when I upgrade to Galleons no one can touch me.
6. Add 1 archer to Jerusalem (it cant be that badly defended. the christian shrine is there, and you give it just 1 archer at the start?? lol. besides, it will still fall at 620ad) I believe the Christian shrine is in Rome. But you can always build military units in-game.
7. Add 3 workers to Iconium (the richest country in Europe in 600AD had only 2 workers -.-): I've found that 2 workers (even when not in Serfdom) are quite sufficient to my needs over the course of the game.
8. Add lighthouse to all coastal cities (you have GREAT lighthouse. you don't even have normal lighthouses?): Can be added in-game, if they are worth the investment. What else are those trashy N. African cities going to build?
9. add 5 workboats (the byzantines were there for so long already and no one thought of working the fishes and clams -.-) Once the land around Athens is improved, it can churn out workboats every other turn. This is not hard to do in-game.
10. Add forge to Constantinople and Athens (i'm sure there's engineers in those cities by 600AD): I can see this as a possibility, though again, I've had no difficulty squeezing in a Forge build during my race to get Cathedrals up.
11. Constantinople size increased to 10 (realistic!) 12. Athens size increased to 5 (same!): If the small sizes bother you, pretend that the empire has just emerged from a catastrophic plague. (Which, in RFC gameplay, is almost certainly true.)
13. Added Oracle to Athens (redundant, but realistic): I could see this.
14. Add Meditation, Philosophy (Byzantium learnt monasticism from the Egyptians very early at like 300AD i think, and philosophy... well the ancient Greeks own at it.) Then you need to revise the tech UHV.
15. Add Jewish temple to Jerusalem (-.-): As a realistic "touch," I can see this. It wouldn't do much good, since happiness and culture are
not problems in Hierousalem.
16. Add granaries to ALL cities (THE RICHEST COUNTRY IN EUROPE 600AD DOESN'T KNOW HOW TO STORE FOOD??!): Granaries are not very important to most of your cities, I think. Except for Constantinopolis, Athens, Alexandria and Cairo (when you add it), most of the cities don't need to grow, and will grow to their natural size pretty quickly. I think it should be player discretion as to when or whether his cities get granaries.
17. Add 6 triremes to Arabian capital (and hope someday they fight): Not realistic. Arabs did not have a powerful navy until after they conquered Egypt. If they conquer Egypt in your game, they will get one.
18. Add Odeon to Constantinople (the capital needs its artists): Maybe. But it would be a Theater, wouldn't it?
Add courthouses to ALL cities!!! (JUST TO SURVIVE TURN 34!!!): I deeply sympathize with the Turn 34 thing. But I've not found that courthouses help. If the hit is big enough, you will take crippling losses despite courthouses. If you don't take crippling losses, then it's because the hit was soft enough on its own.