Drat, my login cookie seems to time out when I'm typing my reply. Maybe that's a sign to not post?
I've yet to get right to the end-game, instead generally restarting around 1000 AD because I hit errors with my save-games or restart as another civ. Thus, my comments on late-game are based on reading what some other people have said, and thinking 'wouldn't X be cool?' to myself.
1) Costs of research and production should steadily go up to a peak level, after which the newer buildings and civics that increase research and production simply maintain, or (very) slightly increase the production speed. Thus, at this peak point you're able to churn things out at a very efficient level, but not instantaneously. However, since things are becoming ever more advanced your old equipment becomes more obsolete, and the longer you don't add to them (ie, new research/production buildings) the slower your research and production will be. A sort-of aside to this might be to start the modern era a bit earlier, making it last longer. Since things won't be getting produced as quickly in it, it won't result in uber-mega military or research, just the prolonging of an interesting era, maybe making the corporations be able to have more effect for a longer period of time too.
2) Blockading of land tiles similar to blockading sea tiles. Islands surrounded by sea can be crippled and starved via a blockade, so why not the land tiles too? This would be more like your traditional seige of a city. Instead of stopping production in one puny tile, you're able to stop it in a number of tiles (perhaps a radius equal to the speed of your fastest unit).
There's mention of a 'Fixed Borders' mod in this forum that does something like this, where a unit 'claims' lands for it's homeland until they're dislodged, depriving the originally owning civ of the benefits of the tiles they've claimed. This can tie into what was mentioned earlier in this thread: Units costing food on top of money (which I support). A special civilian unit called a 'Supply Train', perhaps, could be sent with your military. It would have a finite supply of food for the units to use, and would supplement that with whatever food the surrounding claimed tiles provide. There might be a better version of the 'Supply Train' that can manufacture things using those tiles too, though I can't think of what that would be called. This would result in a 'mini mobile city', feeding and healing the troops, perhaps even making a limited selection of things (seige engines, walls, healing hut?).
3) Work boats should be capturable like land workers. Settlers might perhaps be capturable as well, though I'm less sold on that idea, unless you could capture them, settle a city, and then have their nationality start as what they were initially, like a captured city. It would be as prone to flipping as any captured city of it's initial size, and considered a colony, of sorts.
4) Prisoners of War - Vehicular units would be split in two. The prisoners, which are the operators, and the military unit being rewarded to the capturing nation as their own military unit. The prisoners are the soldiers that are now stripped of defenses and combat ability, which need to be guarded by units or a city and can be sold or traded via diplomacy. Killing a surrendering unit would be greatly frowned on internationally, though perhaps only if some resolution was passed about 'rules of warfare' (can't thing of the blasted real-life term for it). Despotic civs, as one civic example, wouldn't care if you killed the captives, but anyone fighting you would know to fight to the death. Prisoners of war might have a small chance each turn of escaping and either wreaking some havoc or escaping. A pop-up menu would give you an option list similar to the espionage one. You could have them spy on the city, then try to escape to provide you details. Attempt to poison the water, assassinate a unit, free others, or just escape. Each has a percentage chance of escape back to your homelands. Thus, there's a benefit and a negative to keeping P.O.W.s.
5) Expand Terrain in Civipedia to say what can or can't be built on it - Right now, I go into Civipedia to see if I can build anything on desert or tundra or an oasis, and it tells me nothing. No 'buildable improvements are:' This falls more under some other mod's jurisdiction, perhaps.
Thanks for listening to my ramblings. Hopefully they're not utterly ******** and give at least one idea to someone with a brain (and modding knowledge). ;-)