Sometimes I wonder if anybody reads my posts...
I have to repeat myself: The problem with Civilization combat is that it tries to simulate 5000 years of warfare in the single game, which ins't possible without a lot of thought given to mechanics. In fact, the game would need two or three different sets of mechanics - one for pre-1700 warfare and one for after.
SMAC's combat is better because it simulates modern warfare with better tech. Infantry, Rovers, Jets, etc. The combat only changes radically by addition - you get better guns and amor, not go from swords to rifles. You also get new devices that take the war to new places - Foils, Cruisers, Needlejets and Choppers, the more exotic attachments like Drop Pods. Also collateral damage from CivII is less punishing here, so stacking outside cities get you punished, and stacking inside cities make you vulnerable to artillery and mind control. Not to mention the really weird stuff like combat terraforming, psi combat, etc.
Paradox games have a nice answer to the doomstack problem: Supply limit. Translating it to 4X would mean that rather than 1UPT (which is retarded), each type of tile has X number of units allowed, and you can't go beyond the limit or only a penalty. Early wars would be very doomstacky, but eventually tech would make it so that modern units have to scatter and be in many squares rather than concentrate all in a single square- because if they do they either starve to the death or get wiped out by concentrated firepower.
This or a variation of the doomstack that sort of riffs off what Call to Power was doing.
I've never really bothered to totally write it out in detail, but I would very much like a system that utilized 'armies' as actual entities that carry limited slot numbers that you must then fill with infantry, archers, cavalry, etc., all of which are led by generals that confer various bonuses, with singular units being allowed to exist outside the 'armies' yet be less effective (unless, say, a general has an aura that increases their viability like a Hannibal would with cavalry). Said armies could then clash and deal damage based on various attributes the generals give them, as well as the overall make up of the army (5-infantry run into 3-infantry and 2-cavalry, 3-infantry hold the line, 2-cavalry flank and devastate the other army). Battles of annihilation are rare, but constantly reinforcing your armies puts a great deal of stress on the economy/population. Maybe have 'bonuses' to victories that isn't just taking peoples cities: large military victories give your cities happiness, science, gold, respect, whatever. Armies in enemy borders require more resources to support (think attrition in Rise of Nations); without support, an army starts losing slots for a turn (imagine them greyed out).
'Generals' could be much like Spies are in CivV: granted through eras or other means, and numerically increased through the ages so that by the modern era you might have many generals with much larger slot numbers. Said-generals could also earn experience points which is then spent on various pathways. War-like civs would get more generals and/or more slots. An army looking to siege would need to bring siege units, but this would make them necessarily weaker to field battles. Fighters and artillery could bomb armies, taking slots out for a turn as a form of close-air or artillery support. Maybe modern armies actually look like modern armies. Maybe we finally get one of the more devastating killers on the battlefield: the mortar. Mayhaps cities provide support resources for armies, so if you hit a city with bombers you indirectly harm the slots available on the field of battle.
Armies themselves would be supplied by the very resources you always harvest. A Wheat field could be set to feed a city/citizen, or set to feed an army slot. Suddenly, it's worth trading for food stuffs. Iron/Stone are used to help build buildings as sort of tools, or they can be used to help build armies/support slots. Luxury items could help offset the unhappiness of warfare or 'melted down' into slot-support parts in times of dire need (maybe at half-efficiency). "War economies" could be had. Wars of a different nature could take place. The AI would never again need to try and out-duel the player on hexes - which it never, ever will - but instead simplify their processes to simple army/army-support management.
Of course, none of that is ever going to happen. It would require a very different civ game in the first place (I can think of many, many things that would need to be reshaped) and secondly, Civ is based on its simplicity and constant sense of rewarding motion first and foremost. Call to Power tried a variation of the stacks of doom that is very much superior to Civ, but that's not likely to return. I think the suggestion of 'support' hexes which can hold various amounts of units while not allowing stacks of doom is the best and most likely middleground. Civ5's combat system is actually not
that bad, but it is thoroughly and frequently betrayed by the maps upon which it is played, giving players the aforementioned bottlenecks or conga-lines of dudes snaking their way around awkwardly structured landscapes. 1-UPT is simply too restrictive and something of an oddity altogether. Nevermind the strong aesthetic dissonance between 'these hexes represent large tracts of land' and 'this archer can shoot over 3-hexes.'