One of my biggest pet peeves is games like Civilization series not having realistic climate zones based on the geography of the generated world. For example, a desert where you would assume that warm water currents and prevailing winds would produce enough moisture to not be a desert. I’m not a programmer, but I know that it actually wouldn’t be too hard to set a few conditions that help the map generation know where to place certain climates much more accurately.

As for games like Minecraft or maybe the recent Legend of Zelda games, I think that the inaccuracies are part of what makes it fun and interesting. Minecraft has come a long way as well, for example in certain cold mountain biomes they have implemented world generation that produces wide, rounded, deep valleys that indicate prior glaciation.