So I'm actually playing through the old Emerald ROM right now. I'm actually doing a lot of it in order to help generate ideas with my own ROM as I play through it, as well as I'm examining the maps very carefully as I'm playing through the game. I haven't played any pokemon games in a couple years, so if I expect to make a pokemon game, I figured it might be good to get reacquainted with the series.
So as I'm running through Emerald, this is quite seriously the first time I've stopped in the middle of maps at multiple occasions in order to just look at the tiles, admire some of the smaller details, and pay attention to interesting map structures. I've found myself running back and forth through various routes in order to compare the size of the map, to the amount of obstacles, plus the consistency of wild encounters, combined with trainer battles, alongside of how many times I back track in order to heal.
The interesting thing I'm learning from playing through all of this, is that all those factors combined, essentially doubles the playability and time spent within each map. Which is essentially making the maps "feel" larger than they actually are. When I looked at the maps for "Victory Road" in my Emerald ROM, they're actually not that large, but with all the factors that I mentioned above, the maps can take a relatively long time to get through.
I'm starting to realize, that once all those factors that I mentioned are completely implemented into my large map, players are going to be spending an incredibly long time traveling through my large maps, I would even say, probably much longer than what I let alone another actual tester and/or player, would want to spend time on.
I'm quoting your post, because I think my realization might help your question a bit. I will admit, the desert area in Hoenn is rather small, I seriously passed through it in Emerald maybe about a day or two ago, so I think it would be really interesting to see this map in particular extended, since it felt underwhelming and not very exciting or important as a map. However, those other factors that contribute to the map, the more of those that you add, the more time it's going to require a player to spend in.
I'm actually planning now to work with smaller maps in the beginning (wont be using that large 100x100 anymore), as well as I am switching over to Emerald ROM as the base for my game.