People please only post if you're sure of what you're saying!
To obtain one of the Johto starters you must have 200 Pokémon in your Hoenn Pokédex. Jirachi and Deoxys can count towards it but don't have to. Meaning if you have all the Pokémon from Hoenn including Jirachi and Deoxys but are missing say, Roselia and Meditite (2 random examples), your Hoenn Pokédex still has 200 Pokémon and you can obtain one of the 3 'starters'.
edit: Disregard that, Jirachi and Deoxys do not count towards the Hoenn Pokédex completion. You need Pokémon #1-200 in the Hoenn Pokédex for it to be classified as complete and thus be able to obtain your 'starter'.