I like games depicting deeply flawed societies fleshed out in a way so no obvious solutions to all the injustices come to mind.
- Regular egalitarian societies are boring, but introducing a prominent social contract theory into the mix would spice things up.
- Separate courts of law for aristocracy and commoners are getting old. In "The Book of the New Sun" by Gene Wolfe, I liked the way society as a whole was 99% segregated. Middle age society lived in the ruins of space age society (of the same race). The few remainders of the space age society ruled all, while never interacting with the lower classes or even explaining or giving name to their technologies and motives.
Incredible studies exist on how language serves as a framework for our thinking. If a ruling class were to somehow keep the "high language" for themselves, technological and socio-economical advance of the lower classes would stagnate. It wouldn't make peasants dumb, just unable to visualize and develop certain thoughts. While unlikely in the real world, the Project Eternity setting offers magic. If well done, the player character could undergo a memorable transformation from not understanding many parts of his/her world to discovering it fresh)
By the way, I'd much rather have the main quest be internal (PST), instead of external (BG). Wide reaching changes for society should be incidental to choices resulting from personal development.
In fantasy games there is usually a good reason to be religious, because (very human) deities interact with the world. I'd rather not have that. Leave supernatural occurrences inexplicable. Let there be theories, cults and religions, but no proof. Let there be skeptics and believers, and let religion be abused as a political tool.
I'd love to see unique characters, such as the Weaver from China Miéville's "Perdido Street station".
The Weaver, a multi-dimensional being in the form of a giant spider, who speaks in a never-ending torrent of free-verse poetry.
This creature, when encountered, might grant a wish, disembowel and neatly arrange your body parts, talk nonsense, take an ear as a souvenir, or do any combination of the former.
Now that's a cool deity.
- General oddness and setting
There are always scenes so odd and genuinely interesting, that they are never forgotten. Mary Gentle's "Rats and Gargoyles" begins with the public hanging of a dressed pig. The pig was convicted of having eaten a human child that fell into its pen. And since child killers are hanged in ceremonial robes.... well, it left an impression.