To get the Johto starters in Emerald, in-game, first you must complete the entire* Hoenn region Pokedex, than speak with Professor Birch. He will comment on your achievement and allow you to pick one of the three Johto starters.
*Not entire Pokedex, just obtain all of the Hoenn Pokemon excluding Deoxys and Jirachi, or any event Pokemon if l have forgotten any.
(+) This means that you may have to trade Pokemon that can only be obtained in Ruby and Sapphire, since you can't catch all of the Hoenn region Pokemon in Emerald alone.