I'll start. They could do a lot more with Mossdeep Space Center. In a future Hoenn game You could have part of the story take place in space where the enemy team tries to launch a satellite or something and you have to sneak onboard to stop it.

Or it could act as a postgame mission where you can go into orbit to take on Deoxys. Outer space would also be populated by powerful Steel types like Magnezone and Metagross.