Random thoughts...
Hm. I've always thought that the Lake of Rage town was a very early version of Mahogany Town, which may explain why Mahogany town is so small (Plus why would they make two towns that late in the game which are so close together).
This would make sense, because the route would continue to where current Mahogany Town is, and the then the route after it would be some sort of challenge to Blackthorn City (seeing as we've established the possibility that the Ice Path did not exist until much later in development).
The locked house and cave in Violet City exist purely for appearance only, to give the illusion that the Ruins of Alph are there and that you can see past the trees.
The pharmacy in Ecruteak was likely moved because there's just way too much going on there then, so they spread things out and gave more of an incentive to Cianwood City. I do think Cianwood always existed there, because I highly doubt they would make a dead end sea with only the barely accessible whirl islands. Of course Cianwood may have orignially been located further down the coast, rather than on a seperate island.
Oh, and Jasmine's pokemon are stronger than Pryce because she only has the two. Just like with trainers, the less pokemon they have, the stronger they usually are. It's to counter-balance the fact she has barely any pokemon.