I am currently on my 4th game already and after almost 50hrs of gameplay I really have some mods I have in mind that I would loooove to have sooner or later.
I tried standard and epic pacing but the Tech and Civics Trees are just waaaayy to fast in comparison to the production. You can barely make build one unit before it's already too outdated. Settlers and Wonders als also a problem. So my #1 wishlist mod is a slower pacing on the tech & Civics Trees.
#2 turning off of the discrict & general production cost changement: After you reach a certain eara or round (I'm not sure), the production costs of discritcs and their buildings suddenly go waaay up, which i really frustrating and makes you choose to build everything else but discricts. Edit: the production costs in general increase drastically with earas, sometimes I have wonders that take over 50-60 turns in a city that is focused on production.
#3 would be a more reasonable warmonder penalty, especially when you haven't declared war yourself. Right now its like this: if someone declares war on you, you will be the one denounced and hated by everyone. Especially, if you take a city, Even though you never started the war. This is is actually the only real problem I have with the AI so far. (That, and Katherine de Medici always declaring suprise war on me early game XD)
#4 some UI modding. Like building queues and a possibility to see when and which tile will be added to your empire. Maybe even a possibility to choose which tile it will be. Imo, the right side of the UI is not well adjusted. The city production part blocks the view on the other overview in the right corner and it's really annoying to click in and out to get to the part that you actually want.
#5 of cource more leaders and civs^^ my absolute fav that I wish for atm would be Israel, since It propably won't be included into the game as a dlc.