I have the exact same opinion. Kanto and jotho can have upgraded safron/celadon and goldenrod and that would fit. Meanwhile the tropical setting of hoenn makes perfect sense for the region not to have a ginormous capital, with nothing but buildings. What's there left to enjoy? There was no need for a big overhaul but oh well, here it is. But for all those fantastic 7 buildings of the oficial, including a pokecenter, pokemart and a gym, the revamp must have been really big to have mauville become such a metropolis.
On another thought, it's amazing how they did explore all the environments possible, given the tropical setting, and even threw an icy cave in there. From the shore cities of slateport and lillycove to the rustic verdanturf, passing by cities that are suposed to be normal cities like mauville and rustboro, a set of tropical rainforests before and after fortree, some relevant islands like mossdeep and dewford, a desert and volcano environment, this region has it all. If only they had at least 1 more icy location. There's no other region with such a small ice environment besides hoenn. At least the seafoam islands were big. But i think the sheer diversity has a big part on the reason why the hoenn games still are my favorite. The other huge part is the simple fact that the legendaries in RSE were the hardest to find in any other pokemon game. The mystery of how to unlock the sealed chamber and all the regis tombs created a sense of adventure that i never have experienced in any other pokemon game. Sure, finding zapdos at the powerplant nad articuno in the seafoam islands, as well as being able to go and catch the opposing legendary of jotho was really cool but the way the regis are locked is so secretive and i just loved and still love that part of the game. We could get some more mysterious ways to unlock legendaries nowadays.