I like realism, and I've considered the strangeness of time in Civ4 and Civ5 for a long time, but man, phillipeactor, you have a WHOLE lot of requirements. I like some of your ideas, like the idea that walking through the desert might be impossible, or harder, until a certain level of technology, and I would love to see expanded demographies and such.
About battles, though, keep in mind that the battles themselves don't take the full turn, only part of the turn. In 3000 BCE, you might get relatively few major battles over, say, 20 years, whereas later turns are faster, and the units can attack more often. I assume it's harder for a bunch of warriors from Ancient Egypt to recuperate from a battle than it would be for a modern armored unit, too. Hence they'd have more frequent battles.
As for ship movement, if you gave modern warships 50 moves per turn, it'd be completely impossible to defend yourself against them. Consider that a gameplay compromise.
About battles, though, keep in mind that the battles themselves don't take the full turn, only part of the turn. In 3000 BCE, you might get relatively few major battles over, say, 20 years, whereas later turns are faster, and the units can attack more often. I assume it's harder for a bunch of warriors from Ancient Egypt to recuperate from a battle than it would be for a modern armored unit, too. Hence they'd have more frequent battles.
As for ship movement, if you gave modern warships 50 moves per turn, it'd be completely impossible to defend yourself against them. Consider that a gameplay compromise.