to get to johto you have to defeat your rival 1500 times to get to kanto you have to defeat your rival 1000 times to get to hoen defeat your rival 500 times p.s. i know this because i am in the johto...
certain Pokemon like oddish,vulpix,ect. are from the first few games, but are registered in the hoenn pokedex. once u get the national dex it will make more sense