I feel like carpet of doom and stacks of doom are two extremes on opposite sides of the spectrum. Both are bad.
The spectrum from carpet of doom to stacks of doom might look something like this:
Pure 1upt
1upt with no limit on number of units so you get carpet of doom
1upt with soft limit on number of total units on the map (you can exceed limit but suffer penalties)
1upt with hard limit on number of units on the map to prevent carpet of doom. You could make this limit very low but then make units harder to kill so they persist or you could make limit higher (but not carpet of doom levels) and make units easier to kill and you could quickly build replacement units.
Hybrid 1upt
1upt with 1 civilian attached unit
1upt with 1 military or civilian attached unit
1upt where you can merge identical unit types (like corps and armies in civ6).
1upt where you can merge different unit types to create hybrid units.
Stacks
Stacks with a hard limit to a small number (ex: 3 units per stack)
Stacks with hard limit to a bigger number (ex: 15 units per stack)
Stacks with soft limit (you can exceed limit but suffer penalties)
Stacks with no limit so you get stacks of doom
I also think that 1upt and stacks affect how battles would be done:
With pure 1upt, battles will likely be very simplified and tactical. Units will have combat stats and you move units around like a tactical game and each unit maybe damages or kills another unit. With carpet of doom, moving units around becomes very tedious. You get the sliding blocks puzzle problem where it can be tricky to figure out how to move a unit to make space for another unit to move. 1upt with low number of units would make moving units around much easier and if the units are harder to kill, each loss would be more impactful.
With hybrid 1upt, moving multiple units would be easier without going all the way to stacks. With attached units, there might be some micro with battles as you have to click to attach or detach units or select what unit you want to attack with. With merging units, you could have more advanced stats, like a swordsmen-catapult hybrid unit would have both a melee attack stat and a ranged attack stat with bonus to attacking walled cities. You would avoid the micro of attaching and detaching units and you could create specialized units for different military roles, like merging a melee unit with a settler unit to essentially create an armed settler unit.
With stacks, I feel like combat could really take a lot of different forms:
You could do simplified combat where the stack fights as one.
You could make stacked combat a bit more involved where each unit fights one by one in the stack like in civ4.
You could have a tactical combat screen where the player selects battle cards to influence the battle.
You could make each unit a "card" and fight games like a card game, selecting what unit to "play".
You could do a tactical board game style combat like the game Victory & Glory Napoleon where you put units in the left flank, center or right flank boxes and then attack with each unit trying to pierce through enemy lines.
You could do a turn based tactical "chess" type of combat like the game Fields of Glory.
You could do like the game Humankind where your stack spreads out on the map and fight the battles in 1upt format.
You could do a tactical combat screen that works like American football, where you select a formation for your stack and the attacker and defender would select "plays" to try to score damage and win the battle.
You could do like Ultimate General games where you have your units on tactical map and move them in real-time.
You could go full Total War and have a large 3D world where you move your units.
With any type of separate tactical combat you would need an option to auto-resolve for players who don't want to spend a lot of time fighting each battle. I do think one issue with tactical combat in civ is that it could detract from the main game. The focus should be strategic, building your empire, not spending time fighting a tactical battle. And if you do rely on the auto-resolve, then you have to make sure the battle results are fair and transparent to the player.
On of the points of stacks is that you can move everything as a unit. Cuts out a lot of clicks. Maybe I'm misunderstanding?
Yes that is exactly one of the benefits of stacks. And the bigger the stack, the greater the benefit. If your stacks were only 2-3 units, the benefit might not be that big. But if we had big stacks of say 20 units, the benefit would be huge.