Gonna give some extensive feedback on balance and stuff.
Two additional leaders with spies unlocking at Castles may make Catherine's ability feel less unique. Therefore I'm not sure if adding it as part of Elisabeth and Wu Zetian's abilities is a good idea. Alternatively, you could make the bonus loyalty for Elisabeth work for all cities, so not only your own, which might just make the difference in flipping those cities. For Wu Zetian I don't immediately have a good idea, but I don't doubt there's something fun out there. [I hear you, but I think Catherine should still feel unique give her spies are still 'better' - she get's a free spy at Castles, and her spies all get free promotions. Elizabeth 1 and Wu Zetian were both famous for their spies networks, which is part of the reason I've tried to find spy abilities for them.]
Love Isabella's unique ability.
Ship of the Line: 2 bonus strength is very small, 5 might be better. [Yes, probably needs a buff. England's Navy tends to be strong because of the +1 movement and extra great admirals, so I don't want to over do it. I think that was the reason F didn't make the Sea Dog stronger. Anywho, I've buffed SoL to +4. Guess it would need some play testing.]
Berserkers: For the same reason, -3 or -4 might be better. Also because every next point of difference matters more due to the exponential nature of the combat calculations. [Berserkers are a bit rubbish really. Melee 40, up to 47 with attacking, and down to 33 when defending. For comparison, Knights are 48, Pikes are 41, and Samurai are 45. I think maybe Berserkers should just be 40+7 on attack, and then a flat 4 on defence, rather that 40 +7 and 40 -2 as I had them. I've made the change above.]
For the Cree bonus, I'd say that a free Scout in addition to a Warrior is too big an advantage. Maybe just make it instead of? [I thought starting with an extra unit would feel a bit unique. It shouldn't be overpowered give the Cree's unique scout isn't that powerful, and on higher difficulties this boost should even out a little given how many troops the AI starts with.]
Strength in Unity is too strong right now, allowing a possible maximum of 4 attacks (5 if Urban Defenses counts as the next level of Walls). Instead, maybe it's better to add an extra attack to those units at the Tsikhe. [Sorry I meant +1 melee strength per wall level, not +1 attacks. On reflection though, I don't think G needs the further buff given the other buffs to walls.]
Heavy Cavalry change with cards: I presume this is to nerf Knight rushes, but I would argue that arbitrarily removing classes from these cards is not the right way to tackle it. Instead, it's probably better to reduce Knight strength a bit, probably to 44 or 45. That also means Pikemen (51 with the anticav bonus) are significantly stronger, rather than only slightly, meaning the rush is also much easier to counter. [Fair comment. I'll think a bit more. My original thought was that this change wouldn't alter the current balance of units at the level of combat, but instead only at the production level. I also thought this would make Heavy Cav - basically your armies heavy hitters - a little unique.]
Colosseum bonus might be better if it applies to Bread and Circuses in all cities. You'll generally want to build the Colosseum as central as possible to maximize it's area of effect, so the city you build it in is very unlikely to have loyalty problems. On the other hand Colosseum as it is on live is a very strong wonder. [Good point. I've changed that.]
Neighborhood major adjacency bonus might be a little on the strong side. Maybe normal adjacency bonus is better? [You're right. Changed it to Standard.]
Conscription, Levee en Masse (plus some accents): I would argue that these cards not working for Melee units is, if nothing else, against flavour, as conscription was mostly aimed at getting more foot soldiers in the army. To be fair though, I do not see in general why they would apply only to certain classes. [My thinking is that the spearmen line are actually your foot soldiers, whereas melee are more elite or professional soldiers.]
Oligarchy: Science bonus is pretty small right now, I would argue. A typical army in that time (classical, medieval era) will probably consist of, say, 3 swordsmen, 3 crossbowmen, 4 knights. That's 3*36=108 + 3*30=90 + 3*48=144 = 342. That would mean you get 34.2 science - at most two turns worth of science - from winning an entire war. 25% or even 50% might be better. [You're right. I've changed it to 25%.]
I like the Monarchy bonus to loyalty, but would argue it is on the weak side right now. +2 loyalty per level of walls might be better. On the other hand there are several more loyalty buffs in here so stacking them might be too strong. Also the bonus per fort is nice for flavor, but Military Engineers are just far too expensive at the moment. I tend to not even look at them until I want Missile Silos. The general Fort buff is nice though, and might also help for looking at them earlier on. [Agreed. Probably needs play testing.]
I like that you're trying to create more diversity for the military cards. Right now I always go Merchan Republic just because economic slots are just so much better than any others. I often have all economic and wildcard slots filled with economic cards...
Star Chamber should maybe be a bit stronger. -1 amenity will often cost you a happiness level, which then costs you 3 loyalty, so it would be 1 loyalty and losing a bunch of yields. Maybe +6 loyalty instead? [Agreed. Again, probably needs play testing.]
Charter of Rights is really strong right now, specifically when combined with the +2 amenities in all cities with 3 specialty districts card. Maybe better as +1 amenity. [Agreed. Again, probably needs play testing.]
Professional Class is also pretty strong, as it basically removes the gold cost for tier 3 government, just removing the added need to care for your economy. 1 reduction in cost might be more appropiate. [Agreed.]
Village: Would thematically make sense if they gave +1 housing, as there will be more people living in a village than on a farm. Adjacency bonuses should probably also be normal rather than minor, as minor adjacency bonuses don't count unless you have two of them and, well, with the requirements you can't have two villages next to a district. (note that the minor adjacency bonus from, for example, a city center and a woods for a Holy Site doesn't actually stack to give +1 faith) [I didn't want to make housing too easy to get, and also wanted to remain consistent with farms and boats which give 0.5. Village is still strong given it provides adjacencies and also production to flat tiles.]
Mine and Quarry: Would be best to make this malus from, say, Apprentinceship only, and then maybe give an additional production or something. When you only get +1 production from a mine, particularly in the early game, losing food on it just isn't worth it. [I'll give this more thought, but I think players will still build mines because production to so valuable. Either way, I think this will require some more thought and playtesting. I'm also bit worried about how the AI will deal with this change.]
And some ideas of my own: [Thanks!]
-Windmill improvement. Grants +2 gold, grants +1 food to adjacent farms. Grants +1 culture (and tourism) once Conservation (?) is researched. Cannot be built adjacent to one another.
-Leader: Napoleon (France). LUA: Napoleonic Code. +7 loyalty per turn in occupied cities. Cities always generate yields as if they were at full loyalty. [This reflects his reforms in basically every area of society, which laid the foundation for modern values, and also reflects his ability, in many cases, to hold on to conquered land] (I obviously very much disagree with adding only female leaders; I love looking at them, but there's no reason to not add male leaders)
-Bunch of mods that might be nice to integrate into this (of course with permission from the creators): A mod that slows down techs and civics in the late game, AI+, possibly Civ/RF Flavour Deity, and the TSL maps and settlement naming from YnAMP. Maybe Detailed Worlds.
I'll probably come up with some more ideas later on.