I have no idea why we have routes 239 and 240 while they are the exact same routes as 40 and 41.

For the other routes, it would make sense to have them in that order, but I think the idea at the time was that it came after Hoenn (which starts up at 101), so Caldera/Kirant's routes would begin after them. However, since the Johto routes lead to our routes, it might be a good idea to set them up that way, and it shouldn't be hard to implement if enough people support the change.

Kanto and Johto would be far down the line if they were coming. It's something to think about once the game is released, as a manner to make all pokemon catchable.