I'm hearing this, and I'm thinking to myself, "How is this fun?"
All this talk of making it harder to conquer and survive is historically accurate, true. But how is it entertaining, or immersive? It sounds to me like it wouldn't be worth it to even try conquering others with these rules in, and you know what? That makes the game less entertaining, not more, even if it is historically accurate.
The only way these ideas can be made fun is if there is some way to mitigate or eliminate these ideas. Do you know what that means? More options, more in-depth gameplay. Do you know what that means? More work for the developers, and less fun for a good amount of the crowd.
There is an extremely fine line when it comes to historical accuracy. Go too accurate, and the game gets too complex due to too many options. Go too robust or simple, and the game gets too frustrating due to too few options.
Let me give an example which I think may just hit that line.
Imagine you are Germany, in WWII. You simply get up and say, I'm going to take over France. You go in, take over half of France, and turn the second half into a puppet-state, which, in Civ-terms, gives you the rest of France as well. However, the French citizens don't want you there. They riot and resist and do everything in their power to keep you out. But you put down all but the most headstrong partisans through use of obscene amount of soldiers. Although the French don't want you there, they have to put up with you. You have fun - you led a successful invasion.
But now, imagine you are Britain. Your ally, France, has been taken over by the Germans. You eventually mount an invasion, along with your other ally, the Americans, and take France back from Germany. What happens to France next? In some sense, they get their country back. France is reinstated as a Civilization, and Britain and France enter a sort of "Locked Alliance" for a period of turns. In this Alliance, Britain actually extends a large portion of power into France. Their treasuries are combined - all income from both Britain and France go into one account, essentially doubling science for both. They both also get to share their vision with each other. Finally, Britain gets to exert an amount of control over what is built in France, although France does not share the same control over Britain. The only things France gets to keep completely separate is their military units, and their name. Eventually, after a good amount of turns, this locked alliance ends, and the two countries technically part ways, but probably stay allies for a long time. Guess what? You have fun. You saved an ally, destroyed an enemy, and reaped large benefits for it.
What does this do? It keeps it simple, but adds fun by allowing the player control over the details that are meant to make things harder.
Three big things are here:
1. Puppet states. Simple. Others have suggested this.
2. Revolting territories. Simple. Others have suggested this.
3. Saving territories. If someone else has conquered a territory, if you take that territory from them and reinstate it's government, you will be rewarded two-fold. 1. You will weaken your enemy. 2. You will enter a locked alliance with the new nation. Also, if your culture is good enough, that territory may even ask to be entered into your official empire! (Although it would still keep it's own nationality and could differ in it's opinion of your actions from your homeland.)
Always let the players have a limited ability to control these restricting factores, and always have an alternative available, and always keep it as simple as possible. Otherwise, it won't be fun, just frustrating.