Mr.WorldWide
Smugly Inferior
A real example from Civ IV that penalizes stacking is stacked Spies. When there are other friendly Spies present (a stack of Spies) in a plot (tile), the current Spy's mission has a significantly lower chance (~20%) of success.
Something like the above for Civ V's combat system would have been much better than 1UPT or even a maximum of 12 UPT. EDIT: Rather than a fixed stiff penalty of ~20%, the penality should be scaled to no. of units in the stack (maybe -1% per unit).
Sun Tzu Wu
There was a mod for Civ 4 called Defense which toyed with your idea. The more units stacked on a single tile, the weaker they became. Defense shipped with the complete Civ 4 collection.