I'm normally not one for doing this, but I'm going to throw out some wild speculation based on the posts above:
Basically, a Battle Frontier in BW2 would eliminate the need for a Battle Subway. Or at least play it down somewhat. So in case of a Battle Frontier, the facilities residing in the Subway would probably be moved.
This is not to say that the Subway itself would be removed. That would kinda defeat the entire point of Anville town, as well as a couple of the bridges.
My guess is that the Subway would start working like a real subway, taking you to places. Based on the map, Unity Tower would be one of these places. Makes me wonder if subway stations were to be implemented in Black/White from the beginning on, but was left out for some reason.
The other lines would take you elsewhere. Anville, probably the Battle Frontier, places like that. Lots of new places popping up in BW2, not all of them important to the story, but all in all neat places. Not all the destinations would be available upon reaching the station the first time, you would gain access to them as the story progresses.
It might be that the Mistralton Airport will be the gateway to somewhere. Not necessarily Hoenn, but some far-off location. It doesn't have to be an entire region, for all we know, it can be an island somewhere. Perhaps, and only perhaps, the Battle Frontier itself. Yes, that Battle Frontier, but not the rest of Hoenn. If so, the Frontier could be implemented unchanged in RS2 as well, but without the link to Unova. The airport could take you to Mossdeep or wherever.