I think it's tricky. They can't move too far away from the civ mechanic, at least I wouldn't want them to. It's not really possible to simulate an authentic conflict between actual armies in civ's main game, unless perhaps if you move the combat to a secondary battle map, like in AoW or Call to to Power 2. But that wouldn't feel like civ anymore. I think the solution lies in a middle ground between the stacks of doom of pre civ 5 and civ 5's one-unit-per-tile approach. At least it seems like that's what they're trying to do. If it were up to me, I'd allow any combinations to stack, up to three units, and you have to find the combinations that work best. For example, stacking three swordsmen would create three lines of swordsmen on the tile, and only the first line engages in an attack. If they're defeated or damaged, then the 2nd line moves to the front. If however you stack swordsmen with archers/catapults, then the latter would shoot ahead of the attacking line of swordsmen to give them an advantage against a purely swordsmen stack. That's the type of civ I want.

By the way, at least with Civ IV and Civ V, regardless of the stacks of doom or single tile restriction, I find that the conflicts in scenarios feel a lot more actual due to the drastically reduced scale : the whole map is a single region, and a turn typically represents a day/week.