I think it's really hard to pull a space opera off in a pokemon game considering narrative and storytelling is really important for the genre, and pokemon isn't exactly the best medium to tell a heavy story, since you dont have a lot of options with delivery (e.g. you can only primarily use textboxes and you also dont want to dump info on the player). So with that in mind I'd say two worlds intertwined.
Unless Fakemons play an integral part to the story I'd say do not include Fakemons.
NDS mapping is really time consuming and there are no tools actually designed just for NDS mapping like A-Map is for GBA, I'd say keep it simple at first until you get a nice workflow and know how to do everything by heart and then, if it fits the story (so mostly for space opera) redo tilesets and buildings and work with that.
No, I like more unconventional games. Instead of following the standard pokemon formula try to work out a story that still gives motivation for MC to travel the world, but not just "to become the best there ever was".
Just an idea but maybe a messenger sent to prevent a conflict or war between two cities/regions?
Something that shows that NDS does have the capabilities gba has, and that would convince people to actually actively document and research it again.
