While I was playing Diablo III, I've made it to Bastion and just made it to Act IV. . . So the giant fortress gave me the idea to play a Nation RP here. Now, I'm curious as to what would happen if we played a RP where fictional nations in books, and media existed in one world, and were let loose against each other in war.

As per all multiverse crossover NRPs, how do you plan on balancing it without having it be limited or constrained in such a way which takes away from the feel of the nation?

Star Trek vs LOTR won't mesh well as would many fictional Nations. Westeros vs the NCR would be a curbstomp more or less. The Imperium of Man can basically kill anything in sheer numbers. The city in Attack on Titan will never hold against the likes of something like Empire of the Rising Sun. And the GRM would be powerless in the face of the Galactic Empire.

You'd also need to reconcile their in-universe rules and make a very clear set of multi-verse laws. Since one world's rules may not mesh well with another's. The bible for Harry Potter no doubt works much differently from the bible of Lord of the Rings as both would the bible for My Little Pony and then as they would be different from Diablo's or World of Warcraft, you'd have to create some system of magic that would bring the three to a common table.

From a sci-fi perspective too, some systems may or would require specific resources from that universe to work. I don't think the crystal necessary for Jedi Light-sabers would be very common outside of the Galaxy Far Far Away since that's only in George Lucas' head and the Spice of Dune is only in Frank Herbert's. So you'd need to build an opt-in from scratch that still flows with the rules to be built by establishing the previous.

Simple, it won't involve Sci Fi unless it's on the low end. Maybe the Fire Nation, or the Vinci, from Rise of Legends, etcetera. The Ghestalian Empire from Final Fantasy VI is advanced but on the low end of sci fi, they'd be allowed. Shinra from Final Fantasy VII probably won't be allowed, but if they are, they would be the absolute most powerful.