Well, I'm looking at some of the screens for B/W.
If you look at the current areas on serebii for black and white, you can get a better idea of what I'm thinking of.
(I can't post links yet, because I'm a n00b, lol)
Hiun City - I think that this place could hold a flying or water gym. I say this because of the bridges name thats nearby(flying), water(that its a harbor)
Town 2 - Ground type.
City 1 - If Hiun isn't water, this has a high chance of holding a water type gym due to the canals.
Factory - The town near the factory can hold normal, poison, or electric Pokemon. Most Pokemon in shady urban areas are these types.
Forest - Town near this forest can hold bug or grass. However, like in R/S/E, this could just be a forest....
Electric Cave - Town near this could hold electric...
So its Flying, Water, Ground, Posion, Normal, Electric, Bug and Grass.
I also see Dark being thrown in there somewhere as well, as its one of the only types that doesn't have a gym coverage.
For the Elite Four, I would like to see duel types for each E4, kinda similar to what they did in Jhoto.
1.Bug/Grass
2.Psychic/Ghost or Dark
3.Rock/Ground/Steal
4.Water/Ice
5.Let this be like Gary. Have three different fights depending on your starter. I would like to see this champ hold a fight.
Also, let the champion have the ability to be seen around the region for random battles, and let his/her team switch around each fight, but a level increase until you have a team stronger than reds!