I'd happily buy Hoshido and Nohr as separate games if they're significantly different games (i.e. not just opposite sides of the same field for every chapter). If they're same game with minute differences then I'd be hard pressed to justify purchasing both at retail price thusly I'd wait for one of those elusive price drops in Nintendo games.
My biggest concern is the digital version, as I prefer having digital copies of my games. If the purchase then choose a side and you're locked into that is true then I'd be miffed, because I believe (and correct me if I am wrong) you can only purchase a digital game once on a 3ds.
Ultimately I'd love a game, hopefully in digital format, with both versions loaded and playable. Hell for that I'd probably pay console retail price.