Right now, the largest "clue" is definitely Reversal Mountain.
Black City and White Forest made more sense... But a mountain with lava in one and water in another just seems damn weird without Groudon and Kyogre. I mean... They can make some changes ANY other town/city, why must they make it in Reversal Mountain?
I cannot get any clue from the Strange House. That ghost girl is the same one which haunts the Marvelous Bridge. It's like a continuation of that story. I don't find that place bearing any resemblance to the Abandoned Ship.