Culture points for captured Wonders: Should at least be an option in the properties. Real-life wonders fall into the hands of successor states all the time and still manage to be cultural icons!
Annexation: Elimination/Regicide transfers cities. I think this would make for a more realistic conquest mechanic. Sometimes when you cut off the head of the snake, you can surgically attach a new one!
Barbarians can enslave: This would change SO MUCH. You'd have an entire barbarian ecosystem going on, especially if there were more than 1 "barbarian" faction though that's not necessary. You can have barbarian "settlements" that, if they win an invasion, create a new, stronger unit that attacks the civ in revenge. Or barbs that naturally evolve through the course of the game.
Notification/advance warning of reputation ruin: How many times have you tried your best to be diplo-honest only to find out that Civs are snubbing their nose at you over "something" you did? Having the Foreign Advisor warn you beforehand would really help.
Fix for Culture Group: None?/Assign barbs a culture group: This is mostly meant in the case of modded games where barbs have cities that stand in for city-states. Having a non-glitched graphic would be helpful.
No Tile Pollution/TP doesn't affect production: I forgot why I wrote this down, to be honest. It might have something to do with a select few mod scenarios in which "pollution" is something else, like a Mars scenario where the pollution tiles are actually terraforming plants or something and the global warming mechanic creates oceans or something. In case this wasn't obvious, this is more something like an option that can be enabled.
Colonies connect to sea: Now THIS would not only be helpful, it would make sense! Think of all the colonies, fish processing stations, whaling stations, logging etc. that have been put right by a coast with no access to a city. This honestly should have been in the base game, IMO.
Harbor connected by rivers? This is something I've thought about in regards to river-based civilizations for a while. Some ways for rivers to be incorporated economically, I feel there's a lot of underutilized mechanics with them.
Paratroopers have a chance to kill units and can take cities: No reason this shouldn't be possible with an empty city, and if a Paratrooper with an offensive capability got the drop on a weakened unit, they ought to be able to take over that tile.
Editor:
Full LM terrain changes? You ought to be able to say, for example, regular Mountains can't support cities, but LM Mountains can. And all LM variations for all terrains and their corresponding graphics would be cool too. This is more of a suggestion for a modified C3C, because a facsimile like C7 could just as well be able to add entirely new terrain types.
More barbarian evolutions: This would have barbs spawning units that more closely tracked with the era. Combined with barb enslavement, this could have them relevant and a present danger well into the modern period.
Multiple espionage immunities: Speaks for itself and would make a fascinating dynamic.
Change the difficulty of Sabotage and Initiate Propaganda: Initiate Propaganda only
kind of works if you've been trying your very best to win a culture victory, and even then so many things have to go right. And sometimes sabotage only sets work back a turn or so. Reworking these might make these spy actions worthwhile.
Auto and AI razing as a function of government: A 1-pop city has been captured. Should a Democracy really be out here killing entire cities? Maybe for AI civs, razing becomes more of a combination of government type + Civ aggression, and for players capturing a 1-pop they should get the option like any other city if they're under a certain government that's able to control their troops.
Worker AI - Have Terraform flag available even if not all Worker Actions are selected, or do worker actions without flags: AI will use Offense/Defense workers (just Offense seems to work marginally better), but automated player will only use it if they have well defended cities. Other flags will have no action at all. The AI rarely if ever seems to use the Legionary or Crusader's ability to build fortresses (or roads in the Rise of Rome conquest); that might fix it, and we'll be able to have civ-specific worker units that each have different limited actions.