I think that
http://www.bay12games.com/dwarves/dev_future.html is an interesting read.
Some on-topic examples:
WORLD GENERATION PARAMETERS: Allow some degree of control over the world and the more sweeping aspects of play. Possibilities include control over terrain, magic, religions, random vs. stock creatures, fantasy vs. a more 'historical' (ie human) feeling. Ideally, the variability would allow you to move between standard fantasy, fairy tales, mythic fantasy and gothic fantasy, for example. If there are concepts like planes or dimensions implemented, you'd have control over that as well. You could also set the mood -- there's no reason the game needs to be violent at all, for example, assuming the rest of the game can carry it at that point. The world could be generated completely underwater or with no water at all. You could be the first or last sentient creature. There are lots of ways this could go.
PLANES: Once it's all established, you can make regions arbitrarily strange, and you make a lot of them. The real chore here is allowing multiple world maps to be active in one way or another and to allow game elements to move between them. It would be a headache to program, but it would add a lot to the game.
DEITY: Have religions in the game correspond to forces or deities and let you play one and do whatever you like, possibly restricted by your defining characteristics and geography.