What I would like that's actually feasible within the editor we have would probably boll down to cherrypicking things I've most liked from various mods (tech trees as complex as DyP/RaR, something like the Great Cultural Person and reverse-capture-the-flag mechanics from CCM, resource distribution and acquisition through the tech tree something like TETurkhan's Test of Time, and I am forgetting off the top of my head which mod it is that represents the Dark Ages by obsoleting a whole bunch of improvements in ways that smack you down hard) without changing any of the mechanics that actually strike me as just fine (no autogeneration of units, no civilisation or government-specific techs or units, corruption as is is just fine if you throw in more corruption-reducing buildings and more Forbidden-Palace equivalents) and one of these years I am probably going to implement it when I am between jobs.
What I would like in an ideal world where I could pick any feature from any Civ version ever would add onto that by drawing from Civ 2(air units that behave like actual units, none of this "mission" baloney; trade that involves making actual physical caravans and moving them from source to destination; tile improvements that stack, like farming on top of irrigation, but with several iterations of improved mines, for example, and the late-game ability to terraform any tile type into any other), Call to Power (layered maps with undersea and space development as the techs arrive, making for new expansion phases; more kinds of soft/indirect attack), Civ 4 (Corporations, and probably some variation on the religion mechanic), and Civ V(quantitative resources); because what I ideally want from a Civ-type game is something that will on a medium-large map last me about 200 hours of gameplay on a continually changing strategic environment and that is very much geared toward winning at a logistical level, requiring attention towards happiness and culture and science and economics and military and diplomacy and other elements equally, where every problem can ultimately be mastered and solved, and very much not supportive of small-scale tactical combat (which there are dozens of games that do perfectly well already) or towards being winnaible by any purely military approach (because Civ is not Risk.) I love micromanagement, it's most of the joy of the game.
There are a few things that I would hope might be relatively simple with source code access - I'd love to be able to tweak the enslave possibility for Privateers, for example - and others I'm not sure any Civ game has quite got right yet (like hovercraft, or amphibious units capable of moving on land or shallow sea squares only.)