They look exactly the same and have the same Frontier Brains, so I was thinking that maybe they were the same one. Maybe there are just two entrances; one in Sinnoh, and the other in Johto? Was it ever mentioned in the games? The anime says it's in Kanto, but I think that was referring to Emerald's Battle Frontier, which also makes me think: Are there actually 2 Battle Frontiers?
Man, I need to get out more...