Nationalism... Is there really any true downside to using this? Most of my games I see the majority of the world switching to that and sticking with it once they unlock it. We're close to entering the Modern Era in my current game and all but two AIs are running Nationalism and most have been in it since discovering the tech.
So much for spreading the coperation I founded
I'd sort of say the same for Atheism, but the main downside to that one only really pops up if your entire empire has one of every religion in it - though that is easily countered by the massive amount of Happiness you can get, so there's not a lot of downside to it overall. Unless it disabled Religious Buildings as well (Temples, Cathedrals, etc) I don't see why you wouldn't want to run it.
*Edit* Well well, just checked the Info board and it seems all but two leaders are running both Republic and Nationalist.
Myself - Federation + Nationalist
Sitting Bull - Monarchy + Bourgeois
Everyone else, despite sitting at 12 ~ 20+ cities - is running Republic and Nationalist.
I'd post logs, but I forgot how to enable the proper ones that go over these things >< Since I think it's a touch strange that EVERYONE in the game is running Republic and many have been for a very very long time. Most civilizations have quite a few cities, one has just over twenty. I saw Aku Bakr switch into Republic a while ago, and he was getting -870 income until he switched out of it a few dozen turns later (And he's back in Republic now)