I can think of a few things already:
- changes to how cultural borders expand. An ability to choose which tiles are claimed by the city based on culture would be nice (as opposed to it being forcibly computer-controlled). Adding an option to buy tiles further than three tiles away (up to 5 tiles, probably) from the city would also be nice (to make a "buy tiles to establish borders and stop opponents from exploring" tactic viable). I think it would not be too unbalancing if the costs were prohibitive. Additionally, an option to claim tiles only so that they can't be bought by anyone else (so, you can't work them, but you "own" them). Maybe at half price? If you wanted to work that tile later, you'd have to pay the full cost anyway - otherwise, there would be no reason not to "pre-buy" all tiles you can possibly want. Finally, there should be the diplomatic option of buying/selling/trading tiles, if that can be modded in.
- tweak city-states mechanics, perhaps? It would be nice if gaining or losing influence in a city-state increased or decreased influence in other city-states to a minor extent. It's weird that a city that wants their neighbour dead doesn't care that said neighbour has become your ally.
- in Civ 5, buildings seem to follow a strict "development tree", i.e. building A allows the creation of Building B, which is necessary for Building C and so on. This is fine, but since the city development process has much stricter requirements now, more buildings would be nice (for example, Building A allows you to build *either* B1 or B2, and B1 leads to C1 while B2 leads to C2a or C2b), depending on the techs you know.
- optional technologies. I get that Civ 5 has fewer technologies, but the complete lack of technologies that don't need to be taken (like Archery and Horseback Riding in Civ 4, which you didn't strictly *need*, but ended up taking anyway) seems off. A few side technologies that don't lead anywhere, but give you additional bonuses/units/buildings would improve the gameplay experience, I think. Especially as you can't just "fill in the gaps" by trading old technologies with your neighbours, and the choice to ignore a certain tech would have potentially bigger consequences.
These are my thoughts based on a very limited gaming experience, but I already think they would enhance the game if they could be implemented.