I just had an idea for a dungeon. I was looking through the threads and noticed how you had the sea area where only water types can go to and the islands in the sky where flying types can go to. So I was thinking about that it would be nice to have an area a flying type and a water type can reach but no land Pokemon can unless it actually knows surf or gets ferried there.
The idea of the area? A tropical island. One of the dungeons would be a jungle. Make it an ancient one filled with living fossiels. And hey, you can swing around on vines. Nothing more fun than being Tarzan, right?
Another dungeon could be at the beach, making it accessable to fish Pokemon and also other Pokemon. (Really, I feel Pokemon like goldeen, tentacool and such are limited in where they can go to and thus not a lot of people create these fish characters) I suggest pokemon that can live in land and in water to appear in this area then. (Like Krabby, Clamperl, Corfish,... or evo's)
I also just thought off a cave that is half underwater and half above water. Here water Pokemon and other Pokemon could actually work together in exploring it. Maybe some underground ruins?
These are just ideas. In general it would be nice to see some more dungeons for these water pokemon that can't really do anything on land. You don't really have to create them.