Well. Many Possibilities lie in the Quest System, too.
First Quest: Choose between genetic selection or letting things go the way it naturally goes
<You choose option 1> (+10% Growth)
<20 turns later>
Second Quest: Genetic selection has changed your society, new Problems have shown up because the genetic variance was too low. How will you handle them? "Kill all the mutants!!!" or "Try to integrate them into your society." (-10% Energy, +10% science)
<You choose option 1>
<20 turns later>
Third Quest: Mutants have fled into the underground and are now poisoning your water supply. (-20% Health) Produce Soldiers to defeat them!
<20 turns later>
Ending: Soldiers have killed all the mutants and Leela is mourning the death of her parents.
But your Civilization has survived the Mutants! (+20% Culture)
Obviously the example was nonsense, but the quest system could still be used to actually make progress more visible. Of course, introducing new features during the game instead of just developing the existing features would also help.