realistically, a 4x game is about "snowballing" - the more stuff you have the quicker and easier it gets to grab even more stuff. so a decent 4x game needs some mechanics to slow down powers that are in the process of steamrolling the opposition. i always found the temporary unrest of conquered cities a good mechanic. it slows down the aggressor (at least a bit) and it presents you a choice - keep the city and accept that it will suck for the next 50 turns, or raze it and possibly resettle the spot with a new city that starts from scratch.
if there was no penalty, it would be too easy to steamroll right from the beginning - build a few starting units, crush your neighbor and immediately start building even more units from his cities to crush the next guy etc etc.
very well explained! Plus it really makes sense for a conquered city to be that resistant. There are plentoff stories about brave resisters.
by the way, it would be nice to create a fraction/sovereign ability that reduced unrest penalty faster. Something like "Assimilation". In a high-fantasy game it would be typical ability for humans.
Another dynamic that could be fun is to have a chance to spawn rebel armies that try to free the city.