I noticed while reading it seems there are a large number of readers that love game crossovers. I am not referring to the singular game crossover but the ones were three games are placed into the crossover. The primary idea is that each comes from a different timeline and genre reality (I.E. 1 comes from a future reality, 2 comes to a modern or post modern reality, and the 3 comes from a medieval/fantasy reality). In most of these Celestia knows of certain human realities but doesn't know entirely how to treat the main 3 (be it because of lack of knowledge, Xenophobia, or any number of other things). Discord normally either plays a major or minor role as either a friendly ally or primary enemy (as an enemy he always seems to drag monsters from other gaming realities as disposable pawns [the respawning monsters he reuses just as minor entertainment]) (as an ally he gives them items of their reality that they understand but also tries to get them to do stuff that would entertain himself and possibly others). Technology of varying gaming realities could be brought into this as part of the Reality barriers waning and strengthening (this could also be in reference when you are looking for something and you just can never find it).
You can always add new game characters as the story progress (people tend to like the Team Fortress 2 characters [I have found their personalities interesting as will as the unusual abilities {not to mention since they can't be killed permanently the deaths can be a bit comedic in a dark sense}]). Just to note there is more then just Equestria. There is also the Changeling Kingdom, The 13 Griffin City-States, Diamond Dog Land, Dragon Country, The Forgotten Vale, The Wastelands, Everfree Forest (though small can still be used to show some surprises), and many other places should the author come up with anything or do any additional research.