some of my thoughts:
"claiming land" (a bit unsure if this could work out or be pointless)
you might mark tiles that nobody owns as tiles you believe belong to your civ, and when someone is controlling a settler unit, they can see other civs claimed land. as a mechanic to warn others that if they settle these tiles, your hostility will increase towards them, and you might go to war. AI respect this depending on stuff like your friendship, military strenght, the amount of claimed tiles you have (the more you take the less they care) and how close the tiles are to your borders
controlled border growth:
whenever a city's border grow, you choose which tile it takes. when choosing tile, you can also see other players claimed land. can only choose within 3 tile radius, can also be put on automatic.
civilians:
no civilian units except settler and worker. tiles dont give any yield at all unless improved, which is done simply by assigning a citizen to it for a number of turns. workers only build roads, canals, forts and railroads. (I just really dislike having civilian units cluttering up the map).
economy
I'd like to see some kind of different, more complex system of economics. so that you don't earn gold from tiles any more, but in some other way. perhaps have a taxation system which affects both your income and happiness, idk
unit stacking
unit stacking has to be in. I'm gonna say I never played civ4 and don't know the big deal around SoD, but the combat in ciV is such a mess. like when both me and the AI has 10-15 units packed together in some relatively small part of the map at the beginning of a war: it is completely impossible to move units around. strategic positioning goes out the window and all that remains is spamming attacks all you can until the AI can't reinforce anymore. I'd say something like 5-6 military units can go in one tile. units of the same type and mobility can also merge to one, so that all the units in this merged superunit move as one and attack as one (merely making your army much simpler to control, and not affecting combat in any other way, units can dismerge at any time)
strategic resources
I think the game would be much more fun if resources would be distributed differently. rather than being spread around rather randomly, I'd like them to be spread more uniform over the map. each resource contains only 1 quantity, rather than 2, 4, 6 or so on. In ciV I never ever go to war because I lack strategic resources, but I'd like this to be more common.
combat:
rather than strength and ranged strength, have attack and defense. get rid of all promotions that considerably improve an unit: no more range, mobility, logistics, march upgrades. units outside friendly territory cannot normally heal. however, you can use airplanes to airdrop supplies to units, allowing them to heal if they don't perform other actions. also, units standing on road/railroad connected to one of your cities can heal.
allowing land trade in diplomacy
unit cost:
I'm really unsure about this, but have units take away 1 population when produced, and cost food to maintain... would work in with a new economy system. the only type of unit you can buy with money should be a mercenary, which functions like a normal infantry unit except if costs gold rather than food to maintain
canals
if a land tile has ocean on two non-adjacent sides, workers can build a canal through. takes a long time to build, and has high maintenance (other civs may pay you to use your canals)
settling cities and outposts/colonies
when you settle a city, it doesn't start with full health but with 1/3 health. and buying defense buildings shouldn't be possible. when building a fort outside friendly territory, that fort also becomes an outpost/colony, which adds the surrounding tiles to your territory. you can then get these resources without having a city there (this idea needs some work for sure)
specialized infantry:
late game infantry can be promoted to marine/paratrooper (this is not a promotion earned through combat but gained in some other way), so that these are no longer separate units (because there's no need for some many units with little difference between them)