I'll reply to both Tigranes' posts as one.
The most important criterion for what civs went in is that they had to be powerful enough to work within the context of civ the computer game, and they had to be around for long enough to play well. "Spain" and Aragon is actually Castille and Aragon, they become Spain after the union event. There were other Spanish kingdoms as well (including Portugal, originally), but I think this division is enough representation. Bohemia would not be bound to Austria until the 16th century, and in fact a Bohemian king once conquered Austria. But I would not have put in Bohemia unless I was also making a HRE system, in fact if you look on the first or second or so page of the thread I posted the Bohemia would be too weak to work in the game. I think it will work this time around though. Main reason for putting in Lombardy was that I got tired of seeing Genoese Milan, and 40 civs is a nice round number

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It is true that it is slower than the main mod, some of the Python I've written is slower than it needs to be as I've sort of been learning as I went, but mostly it is the inevitable consequence of putting in more civs.
For the new civs I've followed the formula of two historical goals, one "wanted to but didn't" goal. I try too keep the fun and fresh, but it's difficult as you can see from the original Prussia UHV's

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Khazars will not go in since A: I've said that there will be no more civs, and B: Most of their territory is outside the map. Papal states, their UHV would be either nonstop missionary spam or I would have to implement another new system, and I don't feel up to that at the moment.
Kievan Rus - the Mongol invasions have been slightly strengthened, but there is really no guarantee that they collapse. Exception: If you're playing Crimea, they will always be forced to collapse. I've noticed the Bulgarian Lion too and I'm not sure when that happened.
I found the Ushkuiniks while browsing wikipedia, I had no idea before then.
In both your examples probably one of you built the Round Church, it gives diplomacy penalty with other orthodox civs.