Suggestions

[Reliability]

First of all, as we know, the moveset in Topaz is a little...behind compared to the canon games. I'm not going to go off against that. In fact, I have a way to justify it in game. As it stands right now, Caldera-Kirant is pretty underdeveloped technologically compared to the other ones we've seen. The C-K League has just been established before the events of the game, which means that because Caldera-Kirant is so isolated it wouldn't be out of the question that the region's metagame is behind, and hasn't picked up on some of the tactics the other regions have.

This started back before DPP was out, so obviously the metagame will be behind. I think most people will realize that (in reality) we just don't have the man-power to revamp everything when a new region comes out, since we're just so behind as it is. As it said in the FAQ, this is meant to be an alternative to DPP. It just seems like a lot of necessary explanation for something that hasn't really been touched on in any canon game anyway.

Furthermore, we could run with the whole idea of the region being more rural until recently. The western parts of the region have seen an urban boom, resulting in Colussus, Enechestra, etc. Team Rocket has taken control of some things behind the scenes in order to gain more turf. Eastern Kirant would be almost entirely rural, but starting to modernize, with Orion forwarding it...but in much more moderation than Rocket.

Again, seems unnecessary. Going into all this explanation of the past kind of takes away from when the plot unfolds. I'm just envisioning the walls of text as we try to explain all of this properly.

First of all, you might notice that central Caldera is very...chaotic, with two mountains, two cities, and an artificial desert.

Since when is this desert artificial? I was not informed of this... I assumed the the Eye of Sand was a rain shadow off of the mountains.

...Move the Eye of Sand and Saharan City to southwestern Kirant, and remove Portwind. As of right now, Portwind is just filler...IB said it himself. There is no reason to do anything in the southwestern part of the map right now, just sidequests. And since the Eye of Sand was created way back by expy Egyptians, it isn't limited to where it can be. It also moves the 11th Gym closer to the 12th one (Aquapolis), and makes the location of the late game gyms less of a one way path.
I also have a plan for a village to replace Portwind. Soma Island would be expanded into a small village, and would be the location of the Dragon gym. The locals would all have some experience in dragon training, and would stick out a little compared to the visiting trainers and the people running the Gym and Center. This would also give players a reason to explore the southwestern ocean. There just needs to be a plot-related reason to go there in the first place...

We COULD do this, but since the current way is just as good, why would we take the time to change it? I think things are fine the way they are, and side-quests are enough to make people go there. Side quests are, by definition, optional. It will be on the map, people can go there if they want.
If we did what you suggested, it would be best to move Rock to Sedcini and Light to Enechestra. Why? Because that's really the only option, we're running out of viable cities.