I cast my puny vote for turning off civ-specific units and abilities.
From a gaming point of view, I prefer a level playing field: everyone should start off the same. And I prefer my civ to develop in a way determined by me, not according to wired-in special abilities.
From a historical point of view, it's ridiculous to imagine that any primitive tribe in 4000 BC was already preprogrammed with the unique ability to make super-tanks (or whatever) thousands of years down the line.
If such things can be made, it should be possible for any civ to make them. Alternatively, turn 'em all off. That what I'm reckoning to do in my own games.