While this is directly related to VNs, personally I've been hoping to read more stories with the theme of 'cultural and technological exchange'. By that I mean a more developed (Culturally and or technologically) nation/race or individual of one interacting with a less developed one. Ideally it would be in a positive manner, for example teaching them better farming methods, sharing medical knowledge. Also the exchange need not be one way, for example; imagine an Alien race with incredibly advanced technology however everything they create and do is done purely with efficiency and functionality in mind, everything is grey, they don't have any forms of entertainment, nor art, food has no taste only nutritional value and so on. As a result they think and act almost like robots. Then they encounter humanity, who introduces them to their culture, while receiving technology in exchange. As result the Alien race becomes more human-like, happier etc.
As for what kind of separate groups it could be about; Aliens, future/modern day/historic nation, fantasy world race/nation, remote tribe that managed to survive to the modern day with it's culture untouched
A rough outline of how the overall plot could play out; The two groups encounter one another, possible confusion, distrust and/or conflict/skirmishing. They learn to communicate, learn each others language or find/develop another means of communications (Eg magic rings). Exchange of knowledge and technology. Consequences of this exchange; they gain too much power that sparks a war OR perhaps distrust/resentment (perhaps due to casualties from initial encounter) results in conflict between the groups reigniting OR the thing that lead to there encountering each other (eg worm hole, magic portal, dimensional rift) becomes an issue (unstable, will close/shutdown, will destroy both worlds).
Possible content/categories/genres; time travel, parallel worlds, scifi, military/war, fantasy, romance
Some examples I know of; 'Gate: Thus the JSDF Fought There' (LN, Manga), 'StarGate' (Western TV series), 'Zipang' (Manga), 'E? Heibon Desu yo??' (LN, Manga), 'Outbreak Company' (LN, Manga, Anime)
Well in anycase there's a lot that could be done for this kind of story and I'd love to see more like it.