With a good deal of organization, the scripting wouldn't be that hard, actually. I've been thinking and I believe I have a way to implement many of the features. I was considering dropping the random dungeon and simply use the same maps but I think that with some research, it might be possible to examine the Battle Pyramid and possibly devise a similar system. Other than that, I can't seem to find any setbacks. Obviously, there won't be touch compatibility (-_-') but for most everything else, I think I have a way of implementing it (excluding linking moves and the partner-follow system).
The thing is, I prefer the battle system in the normal adventure games to the Mystery Dungeon system so I think I might enjoy a GBA version more than the actual game (which I'm still playing through. Now that I have my emulator running near-perfectly, I've been playing through Platinum, Explorers of Time, and Soul Silver when I get the chance. I had no idea how cool the DS was!).