(Sorry for my English)
This idea is bucking awesome!
I`ve already had this idea too, by playing Empire: Total War. I`ve already drawn a map of the campaign-landscape, Just with other Fractions too. Like Trottland (United Pony-Provinces), Japon, Germaneigh, Flankreich (Prance), Mareway (Scandinavia in Real Life), Griffon Kingdom, Saddle Arabia (which is like the Ottomans), Hooviet Union, United Cities of Tramplevania (Austria in real life) with "ponified" cities etc. Even units like "Brony mercenaries" and stuff.
But like DanTheMan said, the 3d models/animations, would be an BIG problem.
I hope the idea of an "MLP: Total War" mod would eventually implemented.
But I have no idea too, how it works, I can`t even draw a Pony :okiedokielokie: