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Recent? None so far.
Somewhat old? Civilization III. I ordered it like 5 years ago and was trying to scratch the itch left by Call to Power II, but the multiplayer is flaky at best on LAN and the tech tree just isn't interesting to me. Later entries also have the "tech tree doesn't interest me" thing and also don't scratch the Call to Power itch (they don't have the wacky future tech like hover tanks and eco-warfare) but they also look a lot more visually interesting at least.
I miss when stacking was a thing in Civ. Sure it was relatively unbalanced, but that's part of the fun in my experience.
/end grandpa rant
By stacking do you mean combining units to form a single stronger unit? If so, Civ 6 has that, albeit only up to three units.
By stacking, I mean adding the units together on a single tile into armies so the units all fight together. Civ VI does have this, but in a very limited capacity (as you mentioned, up to 3 units). Older games had many more stacking possibilities (Civ III actually had infinite unit stacking, which was cataclysmically crazy lol, but I think Call to Power II really struck a good number with a max of 12 units in a tile)
Civ 3 and 4 would be so much more tolerable if the stacks were limited to something like 12. I haven't been able to go back to those games since 5 changed it up, the stacks of death are too much for me