When writing such a list, you start noticing patterns. I think it is better to just list the design differences than listing all individual changes. Like this:
BALANCE
Units are more expensive to build.
--> Units cannot be build quickly as a reaction to being attacked without having an army yourself.
--> You make a deeper choice, choosing to invest in a building or a unit, as you can't quickly build both.
Units are categorized as Civilian, Ranged, Soldier, Vanguard, Skirmish, Common ships and Escort ships.
Soldier (e.g. Iron units): Most damage, often city attack bonus.
Vanguard (e.g. Spear units): 25% bonus on defense
--> Useful for ...
Skirmish (Mounted): Can move after attacking, 25% penalty attacking cities.
--> Useful for ...
LEADERS
Most leaders are tweaked or revamped, to make them more distinct and fun.
--> Alexander (Greece) gains the Odeon building; when built, receiving 200 Culture instantly.
--> Augustus Caesar (Rome) starts with Iron in the 5 first cities, to encourage expanding and synergy with Legions
...
If you really want a list, because it is so big and because development is happening (albeit really slowly at this point), I think it should be a community-changed list, like a wiki where anyone can edit the list.