I don't understand this mentality. In Super Mario, the later levels are harder than the beginning ones; is that game punishing you for winning?
No, of course not. It's universally accepted in action/shooting/adventure/RPG/racing/etc... games that the difficulty curve needs to point up. Even turn based wargames (Advanced Wars or Panzer General) do that. But whenever someone suggests something like that in Civ, there's always someone complaining about "being punished for winning".
Technically, the late game mechanics in Civ as they are now do up the difficulty curve. The defenses get tougher, you (are supposed to) face more and stronger units, you need to utilize a larger variety of units, new unit types are gradually introduced (naval raiders, air units, nukes, etc), you (are supposed to) need more effort to maintain loyalty, amenities and housing capacity and build more stuff. As I tried to hint with my World War example, the problem is not mechanics, but the AI's inability to use them against you efficiently.
If the AI in its current state will receive the unconditional instruction to gang on the runaway civ every time, most of the games will end in domination victory for a human player
