Sorry, Dan, I can't resist this discussion.
I've thought of this subject in the past and have an alternative method to any kind of limited stacking system. Though, this method also involves overhauling all other systems; like city growth rates, populations, tech costs, production costs, border growth, etc. etc. But, I think it's worth it overall. Also, it probably needs to be a 64 bit application -- no more 32!! If the Civ and BE series were to take another evolutionary leap, such as the one from Civ4 to Civ5, then I think this is what Firaxis may do... especially if they're going to take advantage of 64 bit apps in the future, like other games are doing.
It's similar to what DefiantMars suggested: increase the resolution!
It's simple and clean, and could potentially solve a lot of problems with 1UPT "at the current map scale/resolution we play on". Again, there aren't any big issues with 1UPT, it's mostly the scale of things. If Firaxis took the time to adjust the scale of things and overhaul all other systems, not only would 1UPT be much more functional and enjoyable -- it would feel EPIC... and epic is a nice thing to feel (or rather, a feeling that "should" be expected) with huge 4X games like Civ or BE.
So, basically, take your standard map and shrink it down a little bit more since units will overall be slower (even at a base move rate of 3) and because we don't really need to be controlling 30+ cities. (With a new siege system discussed below, sieging could be a lot more fun and take more time to do, along with the fun had with pillaging the lands and attacking other armies.)
Now, increase the resolution.
The main city tile now takes up 7 tiles!
Cities now have a workable radius that would be roughly equal to 2 tiles on the original, low-res map. (The image above illustrates how each of those hexes can become 7 hexes... but it would probably be best to just smooth it out and make the radius 6 all around.) Also, cities would still be spaced by at least 3 low-res tiles, which means there second outer ring can be shared between neighboring cities, but never their inner ring.
Population growth is more rapid and can get much higher (as said above, all other systems and costs would need adjustment -- but it's worth it.)
Strategic resources no longer have quantities. To get a quantity of 6 iron from a city, you need to improve 6 of them in your territory.
The basic move rate of standard units is 3 (Would equal about 1 hex on the original maps.), mobile units would be 6 or more.
The basic range some units can shoot up to is 3 (Ranged damage is lessened, to make up for higher concentration of potential focus-fire.). Or, maybe they could remain at a range of 2, that would probably be best. Siege would be higher at 3.
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ATTACKING CITIES
With cities taking up 7 tiles, some systems need to be changed to help gameplay -- and most importantly, to make it more fun!
Garrisoned units are no longer invulnerable and now take a decent amount of collateral damage from city tiles that are attacked that they're sitting on. Also, city defenses (of that tile) get increased by the type of unit fortified there. So, you have a core tile and six outer city tiles to place defenders in.
If attackers make it to your city, the sieges can become huge since there are a lot more tiles surrounding a city. No longer will the AI have units waiting around behind others and traffic jams as it tries to flood your lands with its carpet of doom -- it can now take full advantage of them and use better brute force methods. So, usually, certain sides of your city will be focused on, this is where you move your city defenders to the outer rings facing them. If they get too damaged, you can shuffle them with defenders within your city that are behind them and on a safe side (so it's strategically an advantage to surround a city with an attack on all/most sides).
When enough hit points are lost and the defender is defeated, unless another defender occupies the tile before you do (losing the city protection, and now taking normal combat damage instead of only collateral damage), then your attacker can occupy the tile. But, you haven't conquered the city yet! From there, your attacker can attack other adjacent city tiles and the units lose their city protection and take normal attack damage as they would outside the city (though, they receive a regular defense bonus, as one would get if you were on a hill or forest). Only the core tile continues to offer protection to the unit inside -- so you're not attacking the unit there, you're still attacking the city and only causing collateral damage to the unit (if the defender is smart, it's some type of long range, powerful siege unit within the core).
If you conquer the core tile, as you did the outer tile (but the core is tougher) then you've conquered the city and any other defenders within are destroyed. Though, you may need to occupy more of the six outer city tiles first and reduce the city's health more before conquering the core, so you try and flood your units in while the defender is trying to push you out and prevent you from making more "holes".
EDIT: OR, maybe the core tile is never occupied by a unit (the melee attacker remains on its original tile after the attack). That may be better design. The core is the tile which captures the city and where the city ranged-attack is based from. Only the ring of six tiles around it can be occupied. Also, I take back the destruction of opposing units after capture, that would suck! (And be exploitable.) All units remain where they are until they're killed. So, if you conquer a city with defenders remaining, they'll stay there and have a chance to take back the city.
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TERRAIN AND FEATURES
We're basically increasing the resolution of the map, so features of the map will remain proportional. You're NOT going to have more clusters of mountains and hills, more rivers, and more CHOKE POINTS. For a better idea, think of the maps we have now (disregarding the overall size and other things, like city borders, etc.), but units take up only 1/7th of each tile. Getting around would be a whole lot easier and less frustrating. Attacks could be better concentrated on targets instead of units getting jammed up and "waiting in line" to participate in the war. Also, an army or attack force can better conceal themselves before a surprise attack as well.
Rivers would take up a whole tile. Also, they now hinder your movement progression properly and you cross them properly -- by embarking! Also, major rivers could be 2 or more tiles wide with single-tile width rivers branching off of them (greater resolution can create better detail).
With greater "resolution and detail" the flat-looking maps could be given more height and depth with maybe two height levels of hills and two height levels of mountains. It would be a shame for that original hill tile on the low-res map to just become roughly 6-7 hill tiles all at the same height -- it would be much nicer to have 1 or 2 inner tiles be a second level higher than surrounding tiles -- perhaps it could have gameplay effects too, like greater sight and defense bonuses. You can't really do this sort of thing on the low-res maps we have now, the map would quickly fill up too much with more hills and mountains and you wouldn't be able to gradually smooth out the heights as well with the limited amount of tiles.
Maybe even smaller valleys can be introduced and they provide a defense penalty if you're defending from them against an attacker from normal height flatlands... somewhat like the original vanilla Civ5 flatland penalty.
Maybe even the highest hill level tiles can provide ranged units with +1 range/sight for a greater strategic advantage.
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UNITS
Speaking of sight, that would remain the same. The world would be a darker place and you would need to actively scout and keep guard to watch for intruders. As said above, it would be much easier now to conceal attack forces and crash upon an enemy in full force with a wave of units instead of a spearhead. With a much greater amount of workable tiles around cities, perhaps even vision isn't automatically granted within borders. You get two rings of vision around your city, but with the other four rings you would need to have the tile being worked in order to provide vision to it and the adjacent tiles (only a radius of 1). This introduces some more decision making on where to improve and work tiles and where to place guards and maybe fortifications. Otherwise, pillagers can sneak up onto your doorstep -- maybe even barbs can create camps in foggy tiles within your borders if you're not careful (if those foggy tiles are accessible from and adjacent to neutral lands).
Also, unit production rates would be increased a bit again and they could maybe be a little more expendable. Not too much, because you still want the limited amounts of strategic resources and the units they grant to make a meaningful impact on things. (Or, maybe strategic resource tiles could provide very small quantities at times, but probably no more than 4, most would be 2 or 1). You want more toys to play with on these high-res maps; lots of action, lots of fun. It still wouldn't come close to the ratio we have now between low-res tiles and one unit on each of them.
Another improvement would be possible graphics-wise as well: larger unit models with more personality and flavor. Instead of having to represent each unit with an army of "ants", you can have small groups of larger units which really show off their features and textures. They form the "army" when they're all grouped-up adjacent to each other in larger numbers. I understand why they were ants for Civ 5, and I believe it was the best way to go at that scale, but with a higher resolution of tiles, units can be brought to life better and showed-off. (A small part of the big project I'm working on for Beyond Earth rescales everything in the game to really bring out the flavor of everything -- especially those iconic foot soldiers for each affinity! It's a real shame to have them so tiny, for all the units actually, when they contain so many cool features to show off. All the movement rate animations also suck and are being overhauled -- no more lazy quadruped speed for most units, haha.)
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That's it for now... something to maybe inspire more ideas from you guys -- if you like it and want to run with it.