I've experienced unit stacking in SMAC, civ 2 and civ 4 as well as 1UPT in civ 5. Although I voted for 1UPT, I'm going to break it down a bit relating the games I've mentioned:
In SMAC, unit stacking actually worked, because if your unit stack got attacked by 1 unit and you were defeated, the rest of your troops would sustain a 35% damage penalty and it killed already wounded units as well. The only exception was garrisoned units (and unit stacks in bunkers, too, I think), which was good for defending. In turn, SMAC balanced unit quality and quantity very well. The only issue with this combat system was often bad luck, even if your unit was stronger than your opponent, but the development of the reactors alleviates this a little.
In civ 2, it's a bit similar to SMAC, if I can recall, though not always the case.
In civ 4, collateral damage was limited to just siege/artillery gear (and bombers correct me if I'm wrong) and that was the biggest mistake ever. I absolutely hated seeing stacks of units that I could not defeat, unless I had some catapults stored away. The combat system, along with
, was truly broken and there is no way I am returning to civ 4.
In civ 5, I first saw 1UPT and, combined with independent city strength, I found it rather balanced, but a bit inconvenient for attackers. In vanilla, the balance seemed just right but in G&K and BNW, it became much harder to attack enemies unless you had a good mix of ranged and melee units. And of course there's no more complete kills unless your unit has something like over 3 times the strength of its opponent (e.g. tank v scout). Then, going to the industrial era and beyond, fighting becomes more balanced between attacker and defender when artilleries, battleships and bombers are added.