I'd like to see a tomb. A haunted tomb, with trick walls and doors, hidden traps (pitfalls, boulders, switches which makes walls close in and either change your path or cut it off entirely) and maybe even skeletons possessed by ghost Pokemon to act as trainers. They could even add some Distortion World-type features to it as well - rooms where gravity gets turned on its ear and you have to walk along walls, etc.
Naturally, if you made a wrong move, you'd get teleported back to the entrance...or you could white out and wake up in the Pokemon Center as if you'd lost a battle. Depending on the theme and architecture of said tomb, you could have any number of events surrounding it, too. If it was a ruin, you could have the Regis in it, or even Arceus - if you had to collect each of the plates beforehand, those could be used to unlock more of the place as you progressed. Something more akin to a crypt would make a fantastic place for Darkrai to be in.
Pokemon has touched on each of these things in the past, but we've never really had a place where human bodies get buried, be it a modern graveyard or an old-fashioned tomb. Pokemon would surely haunt these places just as readily as their own burial grounds, and could wreak all kinds of mischief pretending to be the spirits of the dead, or making traps that much more unpredictable. Might be a bit dark, but variety is fun, right?