Secrets could solve all kinds of world gen issues. Anything that you want to make possible, but rare, or at least special, could be enabled by secrets. For example, consider megabeasts. Why not make them utter death in worldgen, practically immortal, slaughtering armies if they desire, but then create a secret given by a god of courage that can allow a hero to kill them? That makes a megabeast slayer far more special, and makes the megabeasts more special too.
And any excess caused by secrets might be fixable by secrets. Undead army ravaging the world? Why not find some secret of the Sun that can banish them. Or perhaps your megabeast slaying line of heroes (secret passed down in the family) is making the nation unbeatable in war? A secret of Lies might cause strife and betrayal in the family to disrupt them, causing the secret to die.
Secrets and counter-secrets, is what I'm saying. Forces in the world to keep things potentially stable. And the beauty of this is, with enough rock-paper-scissors, there's plenty of conflicts, and not all of them will necessarily take place in any given world! By that I mean, maybe sometimes the undead army ISN'T beaten by the secret of the Sun. It could, but not this time...
That would make for more world-types that could be genned. AND it would allow for roguelike quests to find the secrets so that YOU can change history and defeat the evil empire.
(None of this is a suggestion, more an observation of the direction Toady seems to be taking)