Civ II/SMAC rules for stacking would solve the "Stack of DOOM" problem, allow congestion-free movement out of battle, and still make spreading out to 1upt tactically relevant.
Of course the Civ II stacking rules need to be adjusted for units not fighting to the death in a single battle anymore, but there are several ways this could be done with increasing penalty to the stack.
0. Units in the stack fight battles individually, best defender each time, with no penalties if a defender is destroyed. The Civ IV system we hate that spawned the SOD.
1. Strongest defender fights each time, and if it dies, the whole stack is destroyed. Stacks are pretty strong, since a full-health unit would almost never die in a single battle, so to destroy a stack would need to fight each unit in the stack multiple times.
2. Strongest defender fights each time, and all units in the stack take a certain amount of collateral damage. Basically all units have the effect of the "Collateral damage" promotions in Civ IV when attacking a stack. This simulates the SMAC system.
3. Strongest defender fights each time, and all units in the stack take the same damage it takes in the battle. This is pretty strongly discouraging stacked combat, since it reduces the entire stack of N units to the defensive strength of the single best defender. I feel this best captures the feel of Civ II stack combat.
Using this {3} system, units could stack up when moving in peacetime and not have the traffic jams of 1UPT, but since there is a simple and intuitive combat penalty (lets stay away from arbitrary percentages of collateral damage or percent strength reductions), players have the incentive to spread out units for battle.
I feel this captures the tactical feel of marching in column for movement, but forming line for battle. This is also not a hard problem for the AI to solve. Also, stacking units in cities and forts negated the penalties, which would make cities easier to defend without bumping up the city strength so drastically as in CiV.
Another issue that popped up in Civ IV is how the player could outmaneuver the AI and take a SOD deep into enemy territory and strike at their capital. We also can learn much from the venerable Civ II in this case as well:
Civ II ZOC rules enabled a realistic border defense, and a very strong chokepoint defense. A unit could not move from one tile adjacent to an enemy unit to another adjacent tile.