Alright, I tested the new version a bit, and there is much improvement.

However, here are some criticisms. I'll post the problems in bullet form:
1. Why did you use the regular Isabella LH for Theodora? Amra already has a reskin for Theodoa in his Byzantium in the Civilization downloads section. Also, he has a Basil II Bulgaroctonos as well.
2. Scenario inaccuracies: Lithuania needs to be nerfed. A lot. Byzantines need strengthening. A lot. Moors still Catholic. A lot.
3. There are nearly no Civilopedia or Sid's tips entries for anything actually, I may do a Civilopedia text file and post it in the next couple of days, but I am not good at Sid's Tips.
4. Diplomacy music. This should be an important part of the next version. A piece of music for each culture would give the mod a lot more feel to it when you're talking to them, instead of that eerie silence.
5. A list should be made of the civs that don't have a unique LH, so that it can easily be taken care of.
6. 2nd UU's maybe a list could be made for future reference as the mod gets more complete to allow easier addition of 2nd UU's.
7. A forgotten civ, maybe the Sicilians can be added with, uh, someone as leader?
8. Whose the Sassanid Persian leader? Kavadh? Never heard of him. Might just be a result of my ignorance though. I would think a better leader for them would be either Yazdegerd II or Yazdegerd III. Yazdegerd II was the emperor of Persia around 451, and is famous for his avid persecution of Christians (Armenians and Georgians and Aghbanians) and Jews to a lesser extent, and also for killing St. Vartan Mamikonian on the battlefield. Yazdegerd III fought against the Arab invaders and was able to hold them off, but after he died, the Persians could not effectively resist the Arabs. Also, maybe the Immortal should be their UU again, since it was still their most important bodyguard unit.
9. Another interesting observation, there are more wonders than actual buildings. Don't know what can be done there, I guess theMiddle ages were all about wonders and less about buildings.
Don't let this long list of criticisms fool you, the mod is much improved.