I'd love to see the exteriors of the gyms revamped to be more multi-purpose buildings like the ones in Black and White, and give more of an idea of what the Gym Leaders do besides gym battles.
The Rustboro gym could be part of the Trainer's School, since Roxanne is a teacher there.
Not sure about Dewford gym, maybe some kind of Surf Lifesaving club/surfing school?
Perhaps the Mauville gym could be a workshop, since Wattson is the tinkering type.
The Lavaridge gym could be a hot-spring.
Petalburg City's...could probably just be a gym, since it's a Normal gym and all.
Fortree's could be a sort of loft/aviary, most of the city is in the trees.
Mossdeep's could be an astronaut training facility, like it was in the anime.
The Sootopolis city gym could be some kind of amphitheatre, since Wallace and Juan are both treat battles like a performance.