It would be kind of silly for the two arenas to have the same scoring though. I don't think it would be a bad idea to "offer a choice" even though in reality, the arena with the better map will be where everyone flies and the other will be left a ghost town.
Scoring is already silly, considering the way people approach the game differently. At least there would be a choice for all of the people that want small or big maps and crowded or dead arenas.