The reasoning to skipping johto is pretty simple. Adding new regions to the game is hard work, and it makes sense for devs to want to maximize what you get from what is added.
Think about itm
Besides the region itself, Emerald gave us a way to capture all the 3rd gen pokemon that cannot be normally caught in fire red. Unova gave us 5th gen pokemon, some 4th gen, and all the items and abilities up to that gen. By adding Sinnoh, we'll finally get a way to capture the 4th gen pokemon that are missing, and you'll effectively the complete assets that existed up the 5th gen.
Johto by comparison doesn't add much. Right now, you can already catch all the 2nd gen pokemon in fire red. Nearly all the moves and items are already in game because of Unova. Soul silver would mainly just add more plot, and areas to walk through, but thats about it.
It's not that they'll never do it, but that theres other additions that give "more bang for the buck" or solve bigger needs for the game.