When it comes to civilians I can agree that they should be allowed to stack.
Unlimited civilian stacking is not completely without a downside. Currently you are only allowed to park one civilian in a single city to safeguard it from attack. It's not a very big threat, usually, but it's there. Unlimited civilian stacking would remove this.
However, there's an alternative stacking rule that could solve most issues: Allow two or more units to stack, civilian or military, provided they all have a different nationality and are not at war with each other. Thus, as far as your units are concerned it's still 1UPT but friendly foreign units won't mess up your troop movements or road constructions.
i.e. 1UPT per nationality.