One unit per tile (together with hexes instead of squares) was IMHO the best improvement that the Civ series could get. Battles in CivV were suddenly a lot about tactics and not just about the size of your military, which made it both fun and realistic. Yes, some details aren't really realistic, becase archers really would be able to stand closer to warriors than tens of kilometers (the size of hexes)

But you have to take this as a tactical battle mini-game inside the civ world. The scale makes no sense, but it's a game, not a simulation. You have to put archers BEHIND warriors, as you would do in a real battle. In Civ this means to put them on the hex behind them.
With the ability to put a ranged and a melee unit on the same tile you would suddenly create a combined unit with ranged abilities (from the archer) and with good melee abilities when defending (from the swordsman), which would break the differentation of unit types and the rock-paper-scissors system.