I think what could make the biggest change is flags being available for EVERY SETTING IN THE EDITOR.
On every single thing you can change, add also the ability to set a flag.
So,
"If IMPROVEMENT = BUILT, then UNIT = AVAILABLE, then AGGRESSION = -2, then REPUTATION = +5", etc, etc. Just being able to link up a bunch of different modifiers, I think, could lead to a lot of new kinds of units, improvements, etc.
Also, a lot more customization for governments -- like being able to set the chances of your civ gaining the cities of neighbouring civs based on government types (Republic takes Despotism, Monarchy takes Republic, Democracy takes Monarchy, Communism takes Democracy under certain conditions (war-weariness, civil disorder flags, etc!)), etc. Also being able to set governments to, once chosen, never declare war, or to have war declared on them by certain other types. And being able to set multiple settings for everything -- let us shun more than one government, and set the intensity of often-built units/improvements instead of just setting them as 'often'.
Being able to set, under improvement's requirements, multiple governments. I don't want despotists to build universities, but I don't want only Monarchists to, either...
Also, let us set units and specialists as government-specific -- and give us more options for them, too. Like a capitalist specialist under democracy to add extra gold but at cost of making a happy content, or a content angry. Or a militia unit for communism, with high defense but no real capability of being an attack unit. Things like that.
...
or, you know what?
Better yet, just give us all the code to program OUR OWN editors, Firaxis.

We'll come up with everything we need, you won't have to deal with disappointments.