I don't know how much the original creators thought about it other than a plot device for a means for Robuttnick to weasel his way into a position of power with King Max. The overall ambiguity of this ominous "Great War" does give me a feeling of wanting to know more; I pretty sure that they were going to cover more about it in the third season that never happened.
However, you can be assured that it would probably be involving two or more factions vying for resources or religious beliefs. When you get down to the nitty gritty those two factors are always at the very basis of all human conflicts. In Sea3on we know of at least one, or possibility of the only the main adversary of the Mobotropolian people: The Warclaws. Though not much has been revealed thus far about the hows and whys of the conflict, either or both of those factors could be the cause of the conflict.
I get the feeling from SatAM and Sea3on that The Great War wasn't going well for Mobotropolis and Julian came in, and with his technology, turned The Great War to their favour. With the order of King Max to "dismantle the military" in Blast to the Past leads me to believe that Mobotropolis might not have had more than a meager defensive force to begin which would leave them wide open for conquest until Julian came to the rescue.
Mobotropolis, just by how it's always referred to as a city rather than a country might be a city-state similar to something found in Ancient Greece; i.e. Athens. Perhaps they were a small "utopian" oasis in an otherwise hostile world filled with many factions that were at eachother's throats and were caught in the fray.
In both Cry of the Wolf and Fed Up with Antoine we were shown two other factions: The Wolfpack and The Nasty Hyenas. Now, it does mention that the Wolfpack is loyal to The King "Max," but The Nasty Hyenas are a pack of wild vagabond cannibals; perhaps they were somehow allied with The Warclaws? Other than the Terapods, which I really wouldn't call a faction, I don't remember any other groups that were not somehow affiliated with Mobotropolis or The King.
As far as geographical areas in SatAM, most seem to be uninhabited by name: The Great Unknown, The Great Forest, The Great Swamp (that has a prison that has been abandoned for over a millennium: Ironlock). Come to think of it a lot of things have "The Great" preceding it in name; perhaps that in and of itself might tell a lot about the Mobian psychology.
Anyway, that's my 2 cents on the topic.