...a one-for-one exactly accurate simulation...
Arguably, that would not be a simulation, but a re-creation of reality itself. But we'll leave that to the philosophers.
If what you want is... the logistical management for World War II, then I doubt that's going to be playable in anything resembling a reasonable amount of time...
It'd be pretty boring, too, sitting here for hours on end clicking on the mouse to install rivets. Although it might be fun when Paris is liberated and the local ladies show their gratitude... then again, that might bump the game rating beyond that accessible to some younger players.
I do not get this emphasis on "realism", considering how many other aspects of the game are simplifying reality to make the game playable.
Consider the following values given for pi:
83.761234701276010236 = very precise, not accurate
3.14 = not so precise, much more accurate
As with precision and accuracy, there is a difference in the quality of a simulation between realism and detail. If I had to order each musketman to load his gun prior to an attack, that would increase the precision while adding nothing to the realism. But if the game required Flight as a prerequisite technology for the Apollo Program, that would increase the realism without adding any (significant) detail.
...if what you are willing to accept is anything less than that, then you have already acknowledged that playability is more important than "realism"
I do agree that playability merits compromising realism. However, this being a simulation, a degree of realism enhances playability.
Imagine if Workers, Settlers, and military units all walked on water, where cities were built amidst floating resources, and only boats could enter land tiles. Imagine if Infantry had a strength of 3, Archery were a prerequisite to build factories, and the most powerful unit in the game were the Chariot (available with Divine Right; requires Bananas).
All of this could be achieved with a few judicious swaps in the XML files, and without changing the
underlying gameplay one iota. But all realism would be lost, the game would be counterintuitive, and it would generally stink. Gameplay would suffer.
Why should you have to attack them with your military, though ? That just puts us right back to military trumping everything else, which is what I am trying to get away from here.
A bit more arguing, then I'll actually try to be helpful:
Does military trump everything else? My perspective is this: It is powerful, useful, and-- if you want to survive--
required. If you are attacked militarily, your defense must absolutely involve military units.
But compare it to other core aspects of the game. You
must build workers, you
must build cities, you
must improve tiles, and you
must research new technologies.
Perhaps you don't absolutely
have to build wonders, culture, and spy points, but you'll be in dire straits without a minimal degree of each.
Now consider this: If I settle my region and improve my tiles intelligently, I get more productive cities. The additional hammers will let me out-produce a militant rival who neglects these details (I will have more units). So city and tile management "trumps" military.
Or: If I research wisely, build +%

buildings, and leverage my traits (more cities with an Organized leader, cottages with Financial, etc.), then I will out-tech a militant rival who neglects these details. Montezuma's massed Jaguars will die
en masse at the barrels of a handful of Riflemen. So tech "trumps" military.
Similarly (although I've never been as good at this): If I have an Espionage advantage, I can instigate revolt, steal technologies, gain significant advance notice of unit types and positions, and even sabotage my rival's strategic resources. Espionage can "trump" military.
But wait! you say, if I may so rudely put words in your mouth,
each of these processes still
terminates in the use of military units. True enough. But that is how all the core aspects of gameplay function. I say again:
All of the core gameplay aspects affect each other, so that the successful use of one leads to the success of another.
I might research Music with the goal of winning a cultural victory. The technology makes it possible, but I cannot neglect the building of cathedrals.
I might go to war to expand my empire with the ultimate goal of winning a space race victory. The conquered cities make it possible (providing more

and

), but I cannot neglect actually doing the research and building the spaceship.
I might vassalize a lukewarm rival and eliminate a hateful rival with the ultimate goal of a diplomatic victory. Military action makes it possible by shifting the balance of rival populations in my favor. But I cannot neglect building the Apostolic Palace, spreading my religion, and calling for votes.
Conquest & Domination Victories
The exceptions to the rule, these victory conditions combine the means (conquest) and ends (conquest). Frankly, I do not like them as they are. At the least, they should be considered "abnormal" game options (like 'Always War' or a modern-era start) instead of being the standard default (which they unfortunately are for HoF and GotM).
Culture
The exception to the other rule. Building, teching, spying, expanding and fighting all provide "universal" benefits. I.e., success in one aspect improves your situation in the others. Not so with culture, and I think this is one of your complaints. If so, I fully agree. There are many reasons for this problem, but I'll reiterate what I think is the most significant one: A city's culture provides no benefit to the rest of the empire; thus specialization is irrelevant and interior culture is worthless.
War happiness is a big gap that needs to be fixed. Some populations really WANT to be at war with certain other populations, and will even get angry if no war materializes. If you are the leader of the Palestinians, try telling your people you've made peace with Israel!!!
Excellent point! I rather think that the same attitude modifiers used by the AI should be visible and relevant for the human player: They would represent your populace's attitude toward those rival civs, and if the attitude is sufficiently negative you should acquire happiness by starting a war (or suffer unhappiness for avoiding one).
Cheers,
Jason