Imperialism is certainly not a good thing for our modern world, but it is something that happened in history, and so I see no reason why a civ game shouldn't be about that. What I would like to see however is some sort of mechanic that makes large empires optimal early game and untenable late game following the advent of modern media and especially the internet and war profitable early game and costly late game following nuclear weapons.
I certainly believe that saying Imperialism should not be the main mechanic for the majority of Civilization's playthrough is ignoring the fact that it worked for thousands of years. If not for nuclear weapons and modern media, we may still be having major wars and India may still be a colony of England.
Another thing that Civ does poorly is represent PTSD. There's a reason it became so commonplace following World War 1: PTSD is far more prevalent with modern weaponry than it was with Ancient, Classical, etc. Soldiers used to be able to sleep soundly at night, as no one could fight in the dark. Now with flashlights soldiers can fight all night. It used to be that if you were killed, it was by an opponent that took time to kill you. They'd have to draw and fire their arrow, load and fire a crossbow bolt, impale you with their pike, it gave soldiers a feeling of control. Now if you poke your head out of a bad corner you could die, and your allies will never know who did it. There's explosions going on 24/7 from guns, artillery, bombs, etc. If we wanted to talk about contributing factors to the fall of imperialism being added to civ to represent our modern age, then PTSD is absolutely necessary.