The problem with limited stacking in either CtP or similar is that it is always optimal to stack maximally. Civ6 gets around that by making stacking very expensive (build 2 or 3 units) for a modest increase in strength. If each unit behaves independently and/or at full strength, there is no reason not to stack as many as you can. Concentrating power is in 99.999% of the time the best thing to do (unless you have rpg area of effects, which I think would feel at out of place in Civ and weren't enough to prevent stacks of doom in Civ4).
Say the only units you can build are warriors and slingers and the limit is 3 per tile. Unless you're army is a single unit or you are fighting such a weak opponent that you don't need to concentrate your forces (in which case the detailed rules of combat don't matter - you'll win massively anyway) then you want to hit that limit and so on a tile you can have
3 warriors
2 warriors and 1 slinger
1 warrior and 2 slingers
3 slingers
and you'll want to keep those units stacked almost always. As an example, look at how stacks of doom were by far and away the best strategy in Civ4. So you might as well consider each four combinations a single unit. By looking at relative strengths, we can call them
warrior
warrior-slinger
slinger-warrior
slinger
which is exactly the same system as in 1UPT except that we have two extra units. Now ask yourselves, would Civ6 be a better game if it was flooded with a ton of units per era like the warrior-slinger or the slinger-warrior? The answer is no, adding useless redundancy is just clutter that makes the game ugly and adds no strategy what so ever.
So if you want limited UpT you need a proper system rather than units behaving independently. The CtP system is even worse in this regard, adding more units in a stack of 9 made each unit fight better (being in a more ideal position on the battle line), so it encouraged the player to stick to full stacks even more. Which, as I've just shown, is identical to a system with 1UpT and tons of very similar units.
IIRC, Civ2 had an interesting system. Unlimited stacking, but if 1 unit died while defending, they would all die. This gives a strong incentive to not stack too much by making the effective defensive value of each unit very weak when stacked. The problem with that is it makes combat hugely random, a single bad dice roll can lose you the entire war even if you had a superior army. This probably isn't balanced, and definitely isn't fun. There's a reason Civ5 changed combat so that it didn't always result in a unit dying, it helps smooth out the luck.
Having limited stacking in a way which is strategically meaningful and fun is hard, and I haven't seen any good proposals for it on these forums or elsewhere.
</end pontification>