First off, civ 4 is great.
but there is so much potential.
Wars shouldn't be fought in 5 years and have no other consequences other then new land for the victor. Rarely has a war been fought and the status-quo at the beginning of the war been maintained. Power shifts occur during wars and civ 5 needs to exemplify these changes. Britain, France, and Germany didn't have the same power they had before World War 2, and due to the War world powers were the USA and USSR. Wars need to set the stage of global diplomacy for the next 100 years and every time a leader makes a decision they take in account what happened to start the last devastating war.
Ideological differences need to be more adamant. You can't have a communist country being best friends with a free market country, it just doesn't work that way. I'm not calling for a cold war between every opposing countries, but when countries both have a similar goal, say to create a sphere of influence or have resource control, and both countries have extremely separate political ideologies, a tense situation between both countries will erupt.
I really don't think newspapers will have headlines complaining about a video game that has exterminations and genocides in it, especially if its called civilization. had it been called something ridiculous like "White Power" or "Europe: 1942" then it would be controversial. But if they use it in historical context it shouldn't be controversial. And most players (i hope) wouldn't use the option that much, and stick to using it as reason to go to war against a nation.
love the idea of random events; need to be more random and more severe though, history never follows a plan.
more resources, everything we use every day is a resource. the reason Egypt was a big deal 3000 years ago was because it had papyrus and the Nile to propel its resources, but as other countries develop their own resources and the technology to use the resources, and when a nation like Egypt does not expand to get other resources, that nation falls in power.
revolutions. They don't have to just be after civic shifts, but just when new leaders are needed in a monarchy, or when a war starts, or when the government is being cruel.