Here's my take on what you did and what yet needs fixing.
Tradition
The default Tradition bonus of +1 food in capital needs to be doubled.
Monarchy (tile buy bonus) could be expanded to provide a culture spread bonus as well, much like the Angkor Wat does (about 50% reduced culture cost of new tiles). Having very few cities and buying tiles will break your bank in no time, regardless of how cheap it is.
Liberty
What you've done with Collective Rule is most awesome, and it allows a brand new city to start pumping out a Settler in the first few turns that it would have practically no growth either way, until the Workers get to it and improve some tiles. Meritocracy, Republic and Representation are all fine, and make Liberty a good choice for a fast-expansion empire.
Honour
Military Caste is pretty useless/expensive for what it gives. I'd think about changing it, but we still have basically no idea how unit maintenance works. I was thinking of making a garrisoned unit free of upkeep, or have a significant discount. Otherwise, the tree is great and needs no work.
Piety
Wouldn't touch anything in it now. And the Mandate of Heaven might be a bit too much in certain situations (a huge India or Egypt would pump out so much happiness and culture policies it's not even funny). Increasing the effectiveness of happy buildings by so much is potentially gamebreaking, since they are already tightly controlled by their huge (and I mean extremely effing big) upkeep. And finally, the whole tree and the end reward are so very solid, I wouldn't try buffing any one part of it.
Patronage
Would not touch this tree at all. If anything, it is currently overpowered. Good thing you have a CS Balance mod as well.
Autocracy
I'd redo Total War to provide a permanent 10% land unit production and strength bonus. I don't like the temporary buff of the current one.
Order
Order works very fine, and it's all worth it for the +5 production for every city in the end. Your change kind of helps against the CS cheese that is so prevalent right now.
Freedom
Small civs focused on culture are extremely vulnerable, especially since the lopsided AI is more keen on chomping up little pups than grouping up against big dogs. The bonus to Universal Suffrage is great, but nothing else should be changed with it.
Rationalism
Don't change Free Thought to 2 science, it will devalue a whole lot of stuff in the game, and will make the Great Scientist Academy once again useless. I'd also reduce the Humanism +2 happy bonus back to +1. Happiness is something that we're supposed to be keeping a very keen eye on. Sure, currently the penalties of negative happiness are meaningless, but that's what patches and mods are for.
Commerce
Increase the Protectionism bonus to count multiples of a single luxury resource, if possible. I do believe the boost to Trade Unions would become HUGE in an empire with a large number of cities, so I'd probably rething the buffing of it.
Again, just my two

.