Trebuchets are neat, but they are overpowered. I'm not sure if you're aware, but in Conquests they changed bombardment units to always attack units in cities. Cats and trebs and cannons don't go for population or improvements until all the defenders are redlined.
That means you need one-third as many bombardment units to redline a city. It used to take about 30 catapult attacks to redline a city with a few pikemen, which usually wasn't practical, but now that takes about 8 trebs, which is brutally effective. 8 trebs and three knights (or worse, one army) can take no losses in obliterating a civ. And you get to keep the cities at full size with improvements instead of burnt shells.
Fascism's pop loss is 1 per city at size 1-6, 2 at size 7-12, 3 at size 13+. As I understand it, it's a one-time penalty and you can just grow it right back.
The notion is that it historically represents "ethnic cleansing" policies often imposed by fascist governments. You should know by now that effects like that are done on a basis of what seems cool, not on how the AIs will handle it. Think volcanoes. Same with the artillery bombardment change - that was directly in response to people complaining that they wanted bigger bang from their artillery. Never mind how horribly it hurts the AIs who can't use it.
I've always built fighters, too, and like you, I don't yet know exactly how to balance between flaks and fighters, either. I've just been putting one of each in each city for the most part. I also turn off animate battles by the time I get into any modern wars, so it's kinda hard to judge the effectiveness of either. One additional detail is that flaks do work for ground defense, MP, and suppressing resistance.
1814 AD might turn out to be not a great finish date for conquest; 'twas certainly possible to do that with cavalry, especially with a few armies. Sounds like you did have fun with the game and the Conquests features including the specialists, at least.