Radical idea:
If you want to make the game have a different objective than who can steamroll whom, or who can out-tech whom, then you need to dismantle the standard VC's and create a VC based on "RP points"
The winner is the most civilized, or the most altruistic ... not the most powerful or the most advanced. "All" we have to do then is to create this entire new RP point system ...

Now some random thoughts:
1. If we want to reduce offensive warfare, we could make unit supply per turn be 100 gold per turn per unit, for example ... when in the borders of a civ that one is at war with (to allow peaceful travel under open borders).
Offensive war would pretty much shut down research at those rates, I would think. If we shut off pillage gold as well, then invasion = stagnation.
Variants include ramping up war costs as number of cities conquered goes up ... so the limited war to settle border issues is still feasible, but the wipe out the opponent war is not.
2. If we want to not have a runaway tech leader ... perhaps we ramp up the cost per column of techs at a more exponential rate. Thus, the gap between the tech leader and the field in terms of techs (but not cummulative beakers) remains more narrow.
So ... what then are we playing for? Maybe some global "most civilized" state ... an aggregation of gold, techs, culture, and population density (not total pop or amount of land), so that small civs also can compete. In which case the gold should be perhaps gold per capita?
If we created such a "most civilized" score, we could assess that at different benchmarks in time (1000 BC, 1 AD, 500 AD, ... etc.) and have winners of the different time competitions. We might also add points for most trade interactions, maybe most named units in play, etc.
All of which assumes that someone besides Cap'n is interested in a game that is primarily RP

dV